WGCNA Results into Functional Enrichment and Biomineralization Toolkit Analysis
Kristen Brown
11/01/2023
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## - Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
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## boundarylibrary(GenomicRanges)## Warning: package 'GenomicRanges' was built under R version 4.3.1## Loading required package: GenomeInfoDb## Warning: package 'GenomeInfoDb' was built under R version 4.3.1library(rrvgo)## Warning: package 'rrvgo' was built under R version 4.3.1library(rtracklayer)## Warning: package 'rtracklayer' was built under R version 4.3.1gff <- rtracklayer::import("../../../data/Pocillopora_acuta_HIv2.genes_fixed.gff3")
gff <- as.data.frame(gff)
dim(gff) # 478988 9## [1] 478988 13names(gff) ## [1] "seqnames" "start" "end" "width"
## [5] "strand" "source" "type" "score"
## [9] "phase" "ID" "transcript_id" "gene_id"
## [13] "Parent"#gff
transcripts <- subset(gff, type == "transcript")
transcripts_gr <- makeGRangesFromDataFrame(transcripts, keep.extra.columns=TRUE) #extract length information
transcript_lengths <- width(transcripts_gr) #isolate length of each gene
seqnames <- transcripts_gr$ID #extract list of gene id
lengths <- cbind(seqnames, transcript_lengths)
lengths <- as.data.frame(lengths) #convert to data frame
#transcriptskegg <- read.table("../../../data/Pocillopora_acuta_HIv2.genes.KEGG_results.txt", sep="", quote="", na.strings=c("","NA"), blank.lines.skip = FALSE, header=FALSE)
colnames(kegg) <- c("gene_id", "KEGG_new") eggnog<- read.delim("../../../data/Pocillopora_acuta_HIv2.genes.EggNog_results.txt") %>% dplyr::rename("gene_id" = X.query) #this file contains all of the go terms, descriptions, kegg, etcgogene <- merge(transcripts, eggnog, by=c("gene_id"), all=T)
gogene <- merge(gogene, kegg, by=c("gene_id"), all=T)geneInfo <- read.csv("../../../output/WGCNA/WGCNA_ModuleMembership.csv") %>% rename(c("X"="gene_id")) #this file was generated from the WGCNA analyses and contains the modules of interest
dim(geneInfo)## [1] 9056 42head(geneInfo) # there are 9056 genes in our gene info file## gene_id
## 1 Pocillopora_acuta_HIv2___RNAseq.g30335.t1
## 2 Pocillopora_acuta_HIv2___TS.g16852.t1
## 3 Pocillopora_acuta_HIv2___RNAseq.g3902.t1
## 4 Pocillopora_acuta_HIv2___RNAseq.26125_t
## 5 Pocillopora_acuta_HIv2___RNAseq.g30339.t1
## 6 Pocillopora_acuta_HIv2___RNAseq.g1893.t1a
## substanceBXH
## 1 Pocillopora_acuta_HIv2___RNAseq.g30335.t1
## 2 Pocillopora_acuta_HIv2___TS.g16852.t1
## 3 Pocillopora_acuta_HIv2___RNAseq.g3902.t1
## 4 Pocillopora_acuta_HIv2___RNAseq.26125_t
## 5 Pocillopora_acuta_HIv2___RNAseq.g30339.t1
## 6 Pocillopora_acuta_HIv2___RNAseq.g1893.t1a
## geneSymbol moduleColor GO.terms
## 1 Pocillopora_acuta_HIv2___xfSc0000003 black -
## 2 Pocillopora_acuta_HIv2___Sc0000019 black <NA>
## 3 Pocillopora_acuta_HIv2___Sc0000024 black -
## 4 Pocillopora_acuta_HIv2___xfSc0000027 black <NA>
## 5 Pocillopora_acuta_HIv2___xfSc0000003 black -
## 6 Pocillopora_acuta_HIv2___xpSc0000387 black <NA>
## GO.description GS.Flat
## 1 Cephalosporin hydroxylase -0.8938616
## 2 <NA> -0.8703992
## 3 negative regulation of glucocorticoid receptor signaling pathway -0.8654331
## 4 <NA> -0.8031322
## 5 Cephalosporin hydroxylase -0.7923300
## 6 <NA> -0.7486964
## GS.Slope p.GS.Flat p.GS.Slope A.blue p.A.blue A.black
## 1 0.8938616 6.237199e-17 6.237199e-17 -0.7595535 9.370626e-10 0.7033576
## 2 0.8703992 3.935296e-15 3.935296e-15 -0.8021221 2.072099e-11 0.7280203
## 3 0.8654331 8.534866e-15 8.534866e-15 -0.8327252 7.190771e-13 0.8197643
## 4 0.8031322 1.872197e-11 1.872197e-11 -0.6460813 1.238589e-06 0.6110681
## 5 0.7923300 5.380480e-11 5.380480e-11 -0.6489457 1.071892e-06 0.6260532
## 6 0.7486964 2.189807e-09 2.189807e-09 -0.7245418 1.251861e-08 0.5895586
## p.A.black A.pink p.A.pink A.red p.A.red A.salmon
## 1 5.003238e-08 -0.5079717 3.136118e-04 0.5461793 8.621764e-05 0.5493866
## 2 9.850552e-09 -0.5580406 5.588970e-05 0.3912476 7.174168e-03 0.4606596
## 3 3.223984e-12 -0.6871953 1.331418e-07 0.5857099 1.901633e-05 0.6306554
## 4 6.467349e-06 -0.5195226 2.156907e-04 0.3849795 8.244607e-03 0.5335939
## 5 3.268094e-06 -0.4246364 3.267736e-03 0.5067724 3.257931e-04 0.5225691
## 6 1.623948e-05 -0.5932834 1.391179e-05 0.5073211 3.201679e-04 0.4832352
## p.A.salmon A.greenyellow p.A.greenyellow A.turquoise p.A.turquoise
## 1 7.680494e-05 -0.4206004 0.0036088091 0.4014156 5.693135e-03
## 2 1.274787e-03 -0.5069432 0.0003240322 0.5585992 5.473805e-05
## 3 2.630902e-06 -0.4696257 0.0009922575 0.4756188 8.360520e-04
## 4 1.342035e-04 -0.4878816 0.0005831033 0.4288370 2.943174e-03
## 5 1.949756e-04 -0.3758520 0.0100488524 0.3274929 2.630349e-02
## 6 6.694607e-04 -0.5024879 0.0003728777 0.4212276 3.553840e-03
## A.cyan p.A.cyan A.brown p.A.brown A.lightcyan p.A.lightcyan
## 1 -0.5156513 0.0002448853 -0.2724246 0.067005147 -0.20868129 0.1639916
## 2 -0.3371169 0.0219615100 -0.3857958 0.008097831 -0.14542134 0.3349001
## 3 -0.5371580 0.0001186079 -0.3575036 0.014720205 -0.23263128 0.1197578
## 4 -0.3530916 0.0160853787 -0.2600132 0.080964328 -0.02080242 0.8908563
## 5 -0.4646844 0.0011401332 -0.1870275 0.213282682 -0.20574983 0.1701296
## 6 -0.3056741 0.0388414830 -0.2403439 0.107635351 -0.12969461 0.3903073
## A.tan p.A.tan A.green p.A.green A.purple p.A.purple
## 1 -0.06448600 0.67027364 -0.09353456 0.53638980 -0.18085374 0.22905312
## 2 -0.23215742 0.12053488 -0.33698108 0.02201832 -0.15688678 0.29776435
## 3 -0.03918235 0.79599531 -0.10400006 0.49156645 -0.33531501 0.02272519
## 4 -0.20543069 0.17080768 -0.23708645 0.11263543 -0.07208354 0.63403175
## 5 -0.08286450 0.58404180 -0.04112274 0.78612412 -0.19030449 0.20522643
## 6 -0.33416974 0.02322207 -0.19419738 0.19593668 -0.11754512 0.43657352
## A.magenta p.A.magenta A.midnightblue p.A.midnightblue A.grey60
## 1 -0.10007037 0.5081662 -0.12708980 0.3999762 -0.13297580
## 2 -0.10585782 0.4838180 -0.12498575 0.4078868 -0.14549121
## 3 -0.09218063 0.5423301 -0.15206967 0.3130297 -0.18989184
## 4 0.05966144 0.6936853 -0.02909643 0.8477805 -0.15162746
## 5 -0.09213198 0.5425442 -0.16879972 0.2621098 0.10058596
## 6 -0.02379712 0.8752604 -0.07154172 0.6365897 -0.08388907
## p.A.grey60
## 1 0.3783249
## 2 0.3346654
## 3 0.2062290
## 4 0.3144555
## 5 0.5059722
## 6 0.5793847geneInfo <- merge(gogene, geneInfo, by=c("gene_id"), all=T)unique(geneInfo$moduleColor)## [1] "purple" NA "pink" "brown" "turquoise"
## [6] "green" "blue" "cyan" "red" "magenta"
## [11] "greenyellow" "black" "tan" "grey60" "salmon"
## [16] "midnightblue" "lightcyan"geneInfo$Length<-lengths$transcript_lengths[match(geneInfo$gene_id, lengths$seqnames)]
head(geneInfo)## gene_id seqnames
## 1 Pocillopora_acuta_HIv2___RNAseq.10002_t Pocillopora_acuta_HIv2___Sc0000013
## 2 Pocillopora_acuta_HIv2___RNAseq.10010_t Pocillopora_acuta_HIv2___Sc0000013
## 3 Pocillopora_acuta_HIv2___RNAseq.1016_t Pocillopora_acuta_HIv2___Sc0000000
## 4 Pocillopora_acuta_HIv2___RNAseq.10171_t Pocillopora_acuta_HIv2___Sc0000014
## 5 Pocillopora_acuta_HIv2___RNAseq.10212_t Pocillopora_acuta_HIv2___Sc0000014
## 6 Pocillopora_acuta_HIv2___RNAseq.10213_t Pocillopora_acuta_HIv2___Sc0000014
## start end width strand source type score.x phase
## 1 4542087 4551503 9417 + AUGUSTUS transcript NA NA
## 2 4639103 4647350 8248 + AUGUSTUS transcript NA NA
## 3 12011843 12030709 18867 - AUGUSTUS transcript NA NA
## 4 1247280 1259813 12534 + AUGUSTUS transcript NA NA
## 5 1847101 1852620 5520 + AUGUSTUS transcript NA NA
## 6 1853508 1854782 1275 - AUGUSTUS transcript NA NA
## ID
## 1 Pocillopora_acuta_HIv2___RNAseq.10002_t
## 2 Pocillopora_acuta_HIv2___RNAseq.10010_t
## 3 Pocillopora_acuta_HIv2___RNAseq.1016_t
## 4 Pocillopora_acuta_HIv2___RNAseq.10171_t
## 5 Pocillopora_acuta_HIv2___RNAseq.10212_t
## 6 Pocillopora_acuta_HIv2___RNAseq.10213_t
## transcript_id Parent seed_ortholog evalue
## 1 Pocillopora_acuta_HIv2___RNAseq.10002_t 45351.EDO27354 2.41e-93
## 2 Pocillopora_acuta_HIv2___RNAseq.10010_t 6087.XP_002166004.2 1.28e-38
## 3 Pocillopora_acuta_HIv2___RNAseq.1016_t <NA> NA
## 4 Pocillopora_acuta_HIv2___RNAseq.10171_t 106582.XP_004539380.1 1.68e-57
## 5 Pocillopora_acuta_HIv2___RNAseq.10212_t <NA> NA
## 6 Pocillopora_acuta_HIv2___RNAseq.10213_t 45351.EDO30046 7.03e-19
## score.y
## 1 317.0
## 2 164.0
## 3 NA
## 4 225.0
## 5 NA
## 6 85.9
## eggNOG_OGs
## 1 COG0666@1|root,KOG0510@2759|Eukaryota,38G7Q@33154|Opisthokonta,3BCDU@33208|Metazoa
## 2 COG0666@1|root,KOG4177@2759|Eukaryota
## 3 <NA>
## 4 2CMEU@1|root,2QQ5W@2759|Eukaryota,38E7N@33154|Opisthokonta,3BF2D@33208|Metazoa,3CTMS@33213|Bilateria,480S2@7711|Chordata,48X2Z@7742|Vertebrata,4A295@7898|Actinopterygii
## 5 <NA>
## 6 2EMZI@1|root,2SRI3@2759|Eukaryota,3ANDN@33154|Opisthokonta,3C1C1@33208|Metazoa
## max_annot_lvl COG_category Description
## 1 33208|Metazoa DZ osmolarity-sensing cation channel activity
## 2 2759|Eukaryota I spectrin binding
## 3 <NA> <NA> <NA>
## 4 33208|Metazoa T CD5 molecule-like
## 5 <NA> <NA> <NA>
## 6 33208|Metazoa S LicD family
## Preferred_name
## 1 TRPA1
## 2 -
## 3 <NA>
## 4 -
## 5 <NA>
## 6 -
## GOs
## 1 GO:0000302,GO:0001580,GO:0002791,GO:0002793,GO:0003008,GO:0003012,GO:0003674,GO:0004888,GO:0005034,GO:0005215,GO:0005216,GO:0005217,GO:0005244,GO:0005245,GO:0005261,GO:0005262,GO:0005488,GO:0005515,GO:0005575,GO:0005623,GO:0005886,GO:0005887,GO:0006810,GO:0006811,GO:0006812,GO:0006816,GO:0006873,GO:0006874,GO:0006875,GO:0006936,GO:0006939,GO:0006950,GO:0006979,GO:0007154,GO:0007165,GO:0007166,GO:0007204,GO:0007600,GO:0007602,GO:0007606,GO:0007610,GO:0007638,GO:0008150,GO:0008324,GO:0009266,GO:0009314,GO:0009408,GO:0009409,GO:0009410,GO:0009416,GO:0009453,GO:0009581,GO:0009582,GO:0009583,GO:0009593,GO:0009605,GO:0009612,GO:0009628,GO:0009636,GO:0009719,GO:0009966,GO:0009967,GO:0009987,GO:0010033,GO:0010035,GO:0010037,GO:0010243,GO:0010378,GO:0010646,GO:0010647,GO:0010817,GO:0014070,GO:0014074,GO:0014832,GO:0014848,GO:0015075,GO:0015085,GO:0015267,GO:0015276,GO:0015278,GO:0015318,GO:0016020,GO:0016021,GO:0016043,GO:0016048,GO:0016324,GO:0019233,GO:0019722,GO:0019725,GO:0019932,GO:0022607,GO:0022803,GO:0022832,GO:0022834,GO:0022836,GO:0022838,GO:0022839,GO:0022843,GO:0022857,GO:0022890,GO:0023041,GO:0023051,GO:0023052,GO:0023056,GO:0030001,GO:0030003,GO:0030424,GO:0031000,GO:0031224,GO:0031226,GO:0031644,GO:0031646,GO:0032024,GO:0032421,GO:0032501,GO:0032879,GO:0032880,GO:0032991,GO:0033554,GO:0033555,GO:0034220,GO:0034605,GO:0034702,GO:0034703,GO:0035556,GO:0035690,GO:0035774,GO:0036270,GO:0038023,GO:0040011,GO:0040040,GO:0042221,GO:0042330,GO:0042331,GO:0042391,GO:0042493,GO:0042542,GO:0042592,GO:0042752,GO:0042802,GO:0042995,GO:0043005,GO:0043052,GO:0043269,GO:0043270,GO:0043279,GO:0043933,GO:0044057,GO:0044070,GO:0044085,GO:0044425,GO:0044459,GO:0044464,GO:0045177,GO:0046677,GO:0046873,GO:0046883,GO:0046887,GO:0046957,GO:0048265,GO:0048518,GO:0048519,GO:0048522,GO:0048523,GO:0048583,GO:0048584,GO:0048878,GO:0050708,GO:0050714,GO:0050789,GO:0050794,GO:0050796,GO:0050801,GO:0050848,GO:0050850,GO:0050877,GO:0050896,GO:0050906,GO:0050907,GO:0050909,GO:0050912,GO:0050913,GO:0050951,GO:0050954,GO:0050955,GO:0050960,GO:0050961,GO:0050965,GO:0050966,GO:0050968,GO:0050974,GO:0050982,GO:0051046,GO:0051047,GO:0051049,GO:0051050,GO:0051179,GO:0051209,GO:0051222,GO:0051223,GO:0051234,GO:0051239,GO:0051240,GO:0051259,GO:0051260,GO:0051262,GO:0051282,GO:0051283,GO:0051289,GO:0051480,GO:0051606,GO:0051641,GO:0051649,GO:0051716,GO:0051930,GO:0051931,GO:0051969,GO:0052129,GO:0055065,GO:0055074,GO:0055080,GO:0055082,GO:0055085,GO:0060089,GO:0060341,GO:0060401,GO:0060402,GO:0061178,GO:0065003,GO:0065007,GO:0065008,GO:0070201,GO:0070417,GO:0070588,GO:0070838,GO:0070887,GO:0071241,GO:0071244,GO:0071310,GO:0071312,GO:0071313,GO:0071407,GO:0071415,GO:0071417,GO:0071466,GO:0071495,GO:0071840,GO:0071944,GO:0072347,GO:0072503,GO:0072507,GO:0072511,GO:0090087,GO:0090276,GO:0090277,GO:0097458,GO:0097553,GO:0097603,GO:0097604,GO:0098590,GO:0098655,GO:0098660,GO:0098662,GO:0098771,GO:0098796,GO:0098862,GO:0098900,GO:0098908,GO:0099094,GO:0099604,GO:0120025,GO:1901698,GO:1901699,GO:1901700,GO:1901701,GO:1902495,GO:1902531,GO:1902533,GO:1903522,GO:1903530,GO:1903532,GO:1903793,GO:1904058,GO:1904951,GO:1990351,GO:1990760
## 2 -
## 3 <NA>
## 4 -
## 5 <NA>
## 6 -
## EC KEGG_ko KEGG_Pathway KEGG_Module KEGG_Reaction
## 1 - ko:K04984 ko04750,map04750 - -
## 2 - - - - -
## 3 <NA> <NA> <NA> <NA> <NA>
## 4 - ko:K13912 ko04970,map04970 - -
## 5 <NA> <NA> <NA> <NA> <NA>
## 6 - ko:K19873 ko00515,ko01100,map00515,map01100 - -
## KEGG_rclass BRITE
## 1 - ko00000,ko00001,ko04040
## 2 - -
## 3 <NA> <NA>
## 4 - ko00000,ko00001
## 5 <NA> <NA>
## 6 - ko00000,ko00001,ko01000,ko04131
## KEGG_TC CAZy BiGG_Reaction
## 1 1.A.4.6.1,1.A.4.6.2,1.A.4.6.3,1.A.4.6.5 - -
## 2 - - -
## 3 <NA> <NA> <NA>
## 4 - - -
## 5 <NA> <NA> <NA>
## 6 - - -
## PFAMs KEGG_new
## 1 Ank,Ank_2,Ank_3,Ank_4,Ion_trans K04984
## 2 Ank,Ank_2,Ank_4,Ank_5,Ion_trans K04984
## 3 <NA> <NA>
## 4 SRCR,Zona_pellucida,ig <NA>
## 5 <NA> <NA>
## 6 LicD <NA>
## substanceBXH geneSymbol
## 1 Pocillopora_acuta_HIv2___RNAseq.10002_t Pocillopora_acuta_HIv2___Sc0000013
## 2 <NA> <NA>
## 3 <NA> <NA>
## 4 Pocillopora_acuta_HIv2___RNAseq.10171_t Pocillopora_acuta_HIv2___Sc0000014
## 5 <NA> <NA>
## 6 <NA> <NA>
## moduleColor
## 1 purple
## 2 <NA>
## 3 <NA>
## 4 pink
## 5 <NA>
## 6 <NA>
## GO.terms
## 1 GO:0000302,GO:0001580,GO:0002791,GO:0002793,GO:0003008,GO:0003012,GO:0003674,GO:0004888,GO:0005034,GO:0005215,GO:0005216,GO:0005217,GO:0005244,GO:0005245,GO:0005261,GO:0005262,GO:0005488,GO:0005515,GO:0005575,GO:0005623,GO:0005886,GO:0005887,GO:0006810,GO:0006811,GO:0006812,GO:0006816,GO:0006873,GO:0006874,GO:0006875,GO:0006936,GO:0006939,GO:0006950,GO:0006979,GO:0007154,GO:0007165,GO:0007166,GO:0007204,GO:0007600,GO:0007602,GO:0007606,GO:0007610,GO:0007638,GO:0008150,GO:0008324,GO:0009266,GO:0009314,GO:0009408,GO:0009409,GO:0009410,GO:0009416,GO:0009453,GO:0009581,GO:0009582,GO:0009583,GO:0009593,GO:0009605,GO:0009612,GO:0009628,GO:0009636,GO:0009719,GO:0009966,GO:0009967,GO:0009987,GO:0010033,GO:0010035,GO:0010037,GO:0010243,GO:0010378,GO:0010646,GO:0010647,GO:0010817,GO:0014070,GO:0014074,GO:0014832,GO:0014848,GO:0015075,GO:0015085,GO:0015267,GO:0015276,GO:0015278,GO:0015318,GO:0016020,GO:0016021,GO:0016043,GO:0016048,GO:0016324,GO:0019233,GO:0019722,GO:0019725,GO:0019932,GO:0022607,GO:0022803,GO:0022832,GO:0022834,GO:0022836,GO:0022838,GO:0022839,GO:0022843,GO:0022857,GO:0022890,GO:0023041,GO:0023051,GO:0023052,GO:0023056,GO:0030001,GO:0030003,GO:0030424,GO:0031000,GO:0031224,GO:0031226,GO:0031644,GO:0031646,GO:0032024,GO:0032421,GO:0032501,GO:0032879,GO:0032880,GO:0032991,GO:0033554,GO:0033555,GO:0034220,GO:0034605,GO:0034702,GO:0034703,GO:0035556,GO:0035690,GO:0035774,GO:0036270,GO:0038023,GO:0040011,GO:0040040,GO:0042221,GO:0042330,GO:0042331,GO:0042391,GO:0042493,GO:0042542,GO:0042592,GO:0042752,GO:0042802,GO:0042995,GO:0043005,GO:0043052,GO:0043269,GO:0043270,GO:0043279,GO:0043933,GO:0044057,GO:0044070,GO:0044085,GO:0044425,GO:0044459,GO:0044464,GO:0045177,GO:0046677,GO:0046873,GO:0046883,GO:0046887,GO:0046957,GO:0048265,GO:0048518,GO:0048519,GO:0048522,GO:0048523,GO:0048583,GO:0048584,GO:0048878,GO:0050708,GO:0050714,GO:0050789,GO:0050794,GO:0050796,GO:0050801,GO:0050848,GO:0050850,GO:0050877,GO:0050896,GO:0050906,GO:0050907,GO:0050909,GO:0050912,GO:0050913,GO:0050951,GO:0050954,GO:0050955,GO:0050960,GO:0050961,GO:0050965,GO:0050966,GO:0050968,GO:0050974,GO:0050982,GO:0051046,GO:0051047,GO:0051049,GO:0051050,GO:0051179,GO:0051209,GO:0051222,GO:0051223,GO:0051234,GO:0051239,GO:0051240,GO:0051259,GO:0051260,GO:0051262,GO:0051282,GO:0051283,GO:0051289,GO:0051480,GO:0051606,GO:0051641,GO:0051649,GO:0051716,GO:0051930,GO:0051931,GO:0051969,GO:0052129,GO:0055065,GO:0055074,GO:0055080,GO:0055082,GO:0055085,GO:0060089,GO:0060341,GO:0060401,GO:0060402,GO:0061178,GO:0065003,GO:0065007,GO:0065008,GO:0070201,GO:0070417,GO:0070588,GO:0070838,GO:0070887,GO:0071241,GO:0071244,GO:0071310,GO:0071312,GO:0071313,GO:0071407,GO:0071415,GO:0071417,GO:0071466,GO:0071495,GO:0071840,GO:0071944,GO:0072347,GO:0072503,GO:0072507,GO:0072511,GO:0090087,GO:0090276,GO:0090277,GO:0097458,GO:0097553,GO:0097603,GO:0097604,GO:0098590,GO:0098655,GO:0098660,GO:0098662,GO:0098771,GO:0098796,GO:0098862,GO:0098900,GO:0098908,GO:0099094,GO:0099604,GO:0120025,GO:1901698,GO:1901699,GO:1901700,GO:1901701,GO:1902495,GO:1902531,GO:1902533,GO:1903522,GO:1903530,GO:1903532,GO:1903793,GO:1904058,GO:1904951,GO:1990351,GO:1990760
## 2 <NA>
## 3 <NA>
## 4 -
## 5 <NA>
## 6 <NA>
## GO.description GS.Flat GS.Slope p.GS.Flat
## 1 osmolarity-sensing cation channel activity 0.1771390 -0.1771390 0.23891908
## 2 <NA> NA NA NA
## 3 <NA> NA NA NA
## 4 CD5 molecule-like 0.4080408 -0.4080408 0.00487819
## 5 <NA> NA NA NA
## 6 <NA> NA NA NA
## p.GS.Slope A.blue p.A.blue A.black p.A.black A.pink p.A.pink
## 1 0.23891908 0.1629611 0.27921156 -0.1713953 0.25473645 0.2921737 0.048802795
## 2 NA NA NA NA NA NA NA
## 3 NA NA NA NA NA NA NA
## 4 0.00487819 0.3067494 0.03812566 -0.3533591 0.01599966 0.4518803 0.001618732
## 5 NA NA NA NA NA NA NA
## 6 NA NA NA NA NA NA NA
## A.red p.A.red A.salmon p.A.salmon A.greenyellow p.A.greenyellow
## 1 -0.3578780 0.01460905 -0.23859599 0.1102968 0.072408214 0.6325010
## 2 NA NA NA NA NA NA
## 3 NA NA NA NA NA NA
## 4 -0.2555844 0.08646359 -0.07221658 0.6334043 -0.002529817 0.9866872
## 5 NA NA NA NA NA NA
## 6 NA NA NA NA NA NA
## A.turquoise p.A.turquoise A.cyan p.A.cyan A.brown p.A.brown
## 1 0.1743321 0.24656320 0.3255466 0.02726341 -0.0423485 0.779905353
## 2 NA NA NA NA NA NA
## 3 NA NA NA NA NA NA
## 4 -0.3683126 0.01178563 0.1981903 0.18672145 0.4041624 0.005341901
## 5 NA NA NA NA NA NA
## 6 NA NA NA NA NA NA
## A.lightcyan p.A.lightcyan A.tan p.A.tan A.green p.A.green
## 1 0.32912540 0.02552022 -0.08600302 0.5698294 -0.31723181 0.0316989
## 2 NA NA NA NA NA NA
## 3 NA NA NA NA NA NA
## 4 -0.07482659 0.62114671 -0.20237587 0.1773978 0.06753155 0.6556508
## 5 NA NA NA NA NA NA
## 6 NA NA NA NA NA NA
## A.purple p.A.purple A.magenta p.A.magenta A.midnightblue p.A.midnightblue
## 1 0.2222434 0.1376812 0.0728760 0.63029807 -0.21575674 0.1498432
## 2 NA NA NA NA NA NA
## 3 NA NA NA NA NA NA
## 4 0.2274620 0.1284425 0.2659033 0.07407973 -0.06964871 0.6455596
## 5 NA NA NA NA NA NA
## 6 NA NA NA NA NA NA
## A.grey60 p.A.grey60 Length
## 1 0.2225084 0.1372005 9417
## 2 NA NA 8248
## 3 NA NA 18867
## 4 0.2116358 0.1579700 12534
## 5 NA NA 5520
## 6 NA NA 1275#Calcification - upregulation (GO terms associated with WGCNA modules demonstrating positive expression in net calcification
#Run the GOSeq function by module color to test for GO term enrichment. Due to high number of enriched GO terms, I am using an adjusted p-value threshold of <0.0001 and using `rrvgo` package to reduce redundancy in list of GO terms.
##Calcification
### Generate vector with names of all genes
ALL.vector <- c(geneInfo$gene_id)### Generate length vector for all genes
LENGTH.vector <- as.integer(geneInfo$Length)### Generate vector with names in just the module we are analyzing
ID.vector <- geneInfo%>%
filter(moduleColor==c("blue","pink","magenta","lightcyan","purple","brown"))%>%
#get_rows(.data[[module]]))%>%
pull(gene_id)## Warning: There was 1 warning in `filter()`.
## ℹ In argument: `==...`.
## Caused by warning in `moduleColor == c("blue", "pink", "magenta", "lightcyan", "purple", "brown")`:
## ! longer object length is not a multiple of shorter object length##Get a list of GO Terms for each module
GO.terms <- geneInfo%>%
filter(moduleColor==c("blue","pink","magenta","lightcyan","purple","brown"))%>%
#filter(get_rows(.data[[module]]))%>%
dplyr::select(GO.terms,gene_id)## Warning: There was 1 warning in `filter()`.
## ℹ In argument: `==...`.
## Caused by warning in `moduleColor == c("blue", "pink", "magenta", "lightcyan", "purple", "brown")`:
## ! longer object length is not a multiple of shorter object lengthhead(GO.terms)## GO.terms
## 1 <NA>
## 2 GO:0000166,GO:0001885,GO:0002064,GO:0002376,GO:0002520,GO:0002521,GO:0002573,GO:0003158,GO:0003674,GO:0003676,GO:0003677,GO:0003697,GO:0003824,GO:0004312,GO:0005488,GO:0005515,GO:0005575,GO:0005622,GO:0005623,GO:0005737,GO:0005794,GO:0005829,GO:0005886,GO:0005975,GO:0005976,GO:0005977,GO:0006073,GO:0006082,GO:0006084,GO:0006089,GO:0006091,GO:0006112,GO:0006139,GO:0006163,GO:0006164,GO:0006629,GO:0006631,GO:0006633,GO:0006637,GO:0006638,GO:0006639,GO:0006641,GO:0006662,GO:0006723,GO:0006725,GO:0006732,GO:0006753,GO:0006790,GO:0006793,GO:0006796,GO:0006807,GO:0007275,GO:0008144,GO:0008150,GO:0008152,GO:0008610,GO:0008611,GO:0009058,GO:0009108,GO:0009117,GO:0009150,GO:0009152,GO:0009165,GO:0009259,GO:0009260,GO:0009605,GO:0009743,GO:0009744,GO:0009888,GO:0009889,GO:0009893,GO:0009987,GO:0009991,GO:0010033,GO:0012505,GO:0015980,GO:0016020,GO:0016053,GO:0016740,GO:0016746,GO:0016747,GO:0018130,GO:0018904,GO:0019216,GO:0019218,GO:0019222,GO:0019432,GO:0019438,GO:0019637,GO:0019693,GO:0019752,GO:0030097,GO:0030099,GO:0030154,GO:0030223,GO:0030224,GO:0030851,GO:0030855,GO:0030879,GO:0031323,GO:0031325,GO:0031667,GO:0032095,GO:0032097,GO:0032098,GO:0032100,GO:0032101,GO:0032103,GO:0032104,GO:0032106,GO:0032107,GO:0032109,GO:0032501,GO:0032502,GO:0032787,GO:0033865,GO:0033866,GO:0033875,GO:0034030,GO:0034032,GO:0034033,GO:0034097,GO:0034285,GO:0034641,GO:0034654,GO:0035337,GO:0035383,GO:0035384,GO:0036094,GO:0042221,GO:0042335,GO:0042587,GO:0042802,GO:0042803,GO:0043167,GO:0043168,GO:0043170,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0043436,GO:0043603,GO:0043604,GO:0044042,GO:0044237,GO:0044238,GO:0044249,GO:0044255,GO:0044260,GO:0044262,GO:0044264,GO:0044271,GO:0044272,GO:0044281,GO:0044283,GO:0044424,GO:0044444,GO:0044464,GO:0045017,GO:0045446,GO:0045540,GO:0046390,GO:0046394,GO:0046460,GO:0046463,GO:0046483,GO:0046485,GO:0046486,GO:0046504,GO:0046890,GO:0046949,GO:0046983,GO:0048037,GO:0048468,GO:0048513,GO:0048518,GO:0048522,GO:0048534,GO:0048583,GO:0048584,GO:0048731,GO:0048732,GO:0048856,GO:0048869,GO:0050661,GO:0050662,GO:0050789,GO:0050794,GO:0050810,GO:0050896,GO:0051186,GO:0051188,GO:0051716,GO:0055086,GO:0055114,GO:0060429,GO:0061028,GO:0062012,GO:0065007,GO:0065008,GO:0070402,GO:0070670,GO:0070887,GO:0071310,GO:0071322,GO:0071324,GO:0071329,GO:0071345,GO:0071353,GO:0071616,GO:0071704,GO:0071944,GO:0072330,GO:0072521,GO:0072522,GO:0080090,GO:0090181,GO:0090407,GO:0090557,GO:0097089,GO:0097159,GO:0097384,GO:0106118,GO:1901135,GO:1901137,GO:1901265,GO:1901293,GO:1901360,GO:1901362,GO:1901363,GO:1901503,GO:1901564,GO:1901566,GO:1901568,GO:1901570,GO:1901576,GO:1901615,GO:1901700,GO:1901701,GO:1902321,GO:1902930,GO:1903131
## 3 -
## 4 -
## 5 GO:0003674,GO:0003824,GO:0004620,GO:0004622,GO:0004623,GO:0005575,GO:0005576,GO:0005615,GO:0005622,GO:0005623,GO:0005737,GO:0005829,GO:0006629,GO:0006644,GO:0006650,GO:0006793,GO:0006796,GO:0006807,GO:0008150,GO:0008152,GO:0009987,GO:0016298,GO:0016787,GO:0016788,GO:0019637,GO:0036149,GO:0036151,GO:0036152,GO:0044237,GO:0044238,GO:0044255,GO:0044421,GO:0044424,GO:0044444,GO:0044464,GO:0046470,GO:0046486,GO:0046488,GO:0052689,GO:0071704,GO:0097164,GO:1901564
## 6 GO:0000166,GO:0003674,GO:0003824,GO:0003995,GO:0003997,GO:0005102,GO:0005488,GO:0005504,GO:0005515,GO:0005575,GO:0005622,GO:0005623,GO:0005737,GO:0005777,GO:0005782,GO:0005829,GO:0006082,GO:0006091,GO:0006605,GO:0006625,GO:0006629,GO:0006631,GO:0006635,GO:0006690,GO:0006692,GO:0006693,GO:0006694,GO:0006699,GO:0006810,GO:0006886,GO:0006996,GO:0007031,GO:0008104,GO:0008150,GO:0008152,GO:0008202,GO:0008206,GO:0008289,GO:0008610,GO:0009056,GO:0009058,GO:0009062,GO:0009987,GO:0010817,GO:0010941,GO:0010942,GO:0015031,GO:0015833,GO:0016042,GO:0016043,GO:0016053,GO:0016054,GO:0016137,GO:0016138,GO:0016402,GO:0016491,GO:0016627,GO:0016634,GO:0016725,GO:0019395,GO:0019748,GO:0019752,GO:0030258,GO:0031406,GO:0031907,GO:0031974,GO:0032787,GO:0033036,GO:0033293,GO:0033365,GO:0033539,GO:0033540,GO:0033559,GO:0033791,GO:0034440,GO:0034613,GO:0036094,GO:0042445,GO:0042446,GO:0042579,GO:0042802,GO:0042803,GO:0042810,GO:0042811,GO:0042886,GO:0043167,GO:0043168,GO:0043177,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0043233,GO:0043436,GO:0043574,GO:0044237,GO:0044238,GO:0044242,GO:0044248,GO:0044249,GO:0044255,GO:0044281,GO:0044282,GO:0044283,GO:0044422,GO:0044424,GO:0044438,GO:0044439,GO:0044444,GO:0044446,GO:0044464,GO:0044550,GO:0045184,GO:0046394,GO:0046395,GO:0046907,GO:0046983,GO:0048037,GO:0048518,GO:0048522,GO:0048583,GO:0048584,GO:0050660,GO:0050662,GO:0050789,GO:0050794,GO:0051179,GO:0051234,GO:0051641,GO:0051649,GO:0055114,GO:0065007,GO:0065008,GO:0070013,GO:0070727,GO:0071702,GO:0071704,GO:0071705,GO:0071840,GO:0072329,GO:0072330,GO:0072594,GO:0072662,GO:0072663,GO:0080134,GO:0097159,GO:1901135,GO:1901137,GO:1901265,GO:1901360,GO:1901362,GO:1901363,GO:1901568,GO:1901575,GO:1901576,GO:1901615,GO:1901617,GO:1901657,GO:1901659,GO:1902882,GO:1902884,GO:1904069,GO:1904070
## gene_id
## 1 Pocillopora_acuta_HIv2___RNAseq.11323_t
## 2 Pocillopora_acuta_HIv2___RNAseq.16666_t
## 3 Pocillopora_acuta_HIv2___RNAseq.20930_t
## 4 Pocillopora_acuta_HIv2___RNAseq.20979_t
## 5 Pocillopora_acuta_HIv2___RNAseq.23897_t
## 6 Pocillopora_acuta_HIv2___RNAseq.24210_t##Format to have one goterm per row with gene ID repeated
split <- strsplit(as.character(GO.terms$GO.terms), ",")
split2 <- data.frame(v1 = rep.int(GO.terms$gene, sapply(split, length)), v2 = unlist(split))
colnames(split2) <- c("gene", "GO.terms")
GO.terms <- split2##Construct list of genes with 1 for genes in module and 0 for genes not in the module
gene.vector=as.integer(ALL.vector %in% ID.vector)
names(gene.vector)<-ALL.vector#set names
#weight gene vector by bias for length of gene
pwf <- nullp(gene.vector, ID.vector, bias.data=LENGTH.vector) ## Warning in pcls(G): initial point very close to some inequality constraints
#run goseq using Wallenius method for all categories of GO terms
GO.wall <- goseq(pwf, ID.vector, gene2cat=GO.terms, test.cats=c("GO:BP", "GO:MF", "GO:CC"), method="Wallenius", use_genes_without_cat=TRUE)## Using manually entered categories.## Calculating the p-values...## 'select()' returned 1:1 mapping between keys and columnsGO <- GO.wall[order(GO.wall$over_represented_pvalue),]
colnames(GO)[1] <- "GOterm"#adjust p-values
GO$bh_adjust <- p.adjust(GO$over_represented_pvalue, method="BH") #add adjusted p-values#Filtering for p < 0.00001
GO <- GO %>%
dplyr::filter(bh_adjust<0.00001) %>%
dplyr::arrange(., ontology, bh_adjust)
#Write file of results
write.csv(GO, file = "../../../output/WGCNA/goseq_pattern_calcification.csv")module_vector <- c(levels(geneInfo$moduleColor))
ontologies <- c("BP", "MF")go_results <- read.csv("../../../output/WGCNA/goseq_pattern_calcification.csv")
head(go_results)## X GOterm over_represented_pvalue under_represented_pvalue numDEInCat
## 1 1 GO:0000122 0 1 16
## 2 2 GO:0000209 0 1 8
## 3 3 GO:0000280 0 1 14
## 4 4 GO:0000375 0 1 9
## 5 5 GO:0000377 0 1 9
## 6 6 GO:0000398 0 1 9
## numInCat
## 1 16
## 2 8
## 3 14
## 4 9
## 5 9
## 6 9
## term
## 1 negative regulation of transcription by RNA polymerase II
## 2 protein polyubiquitination
## 3 nuclear division
## 4 RNA splicing, via transesterification reactions
## 5 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile
## 6 mRNA splicing, via spliceosome
## ontology bh_adjust
## 1 BP 0
## 2 BP 0
## 3 BP 0
## 4 BP 0
## 5 BP 0
## 6 BP 0go_results <- go_results%>%
filter(ontology=="BP")%>%
filter(bh_adjust != "NA") %>%
filter(numInCat>10)%>%
arrange(., bh_adjust)
head(go_results)## X GOterm over_represented_pvalue under_represented_pvalue numDEInCat
## 1 1 GO:0000122 0 1 16
## 2 3 GO:0000280 0 1 14
## 3 7 GO:0000904 0 1 16
## 4 8 GO:0001101 0 1 13
## 5 9 GO:0001505 0 1 11
## 6 17 GO:0001933 0 1 12
## numInCat term ontology
## 1 16 negative regulation of transcription by RNA polymerase II BP
## 2 14 nuclear division BP
## 3 16 cell morphogenesis involved in differentiation BP
## 4 13 response to acid chemical BP
## 5 11 regulation of neurotransmitter levels BP
## 6 12 negative regulation of protein phosphorylation BP
## bh_adjust
## 1 0
## 2 0
## 3 0
## 4 0
## 5 0
## 6 0library(rrvgo)
#Reduce/collapse GO term set with the rrvgo package
simMatrix <- calculateSimMatrix(go_results$GOterm,
orgdb="org.Ce.eg.db", #c. elegans database
ont="BP",
method="Rel")## ## preparing gene to GO mapping data...## preparing IC data...#calculate similarity
scores <- setNames(-log(go_results$bh_adjust), go_results$GOterm)
reducedTerms <- reduceSimMatrix(simMatrix,
scores,
threshold=0.7,
orgdb="org.Ce.eg.db")
head(reducedTerms)## go cluster parent score size
## GO:1901615 GO:1901615 59 GO:1901615 Inf 1
## GO:0051301 GO:0051301 55 GO:0051301 Inf 162
## GO:0021700 GO:0021700 42 GO:0021700 Inf 0
## GO:0009987 GO:0009987 39 GO:0009987 Inf 0
## GO:0007155 GO:0007155 26 GO:0007155 Inf 58
## GO:0006790 GO:0006790 21 GO:0006790 Inf 9
## term
## GO:1901615 organic hydroxy compound metabolic process
## GO:0051301 cell division
## GO:0021700 developmental maturation
## GO:0009987 cellular process
## GO:0007155 cell adhesion
## GO:0006790 sulfur compound metabolic process
## parentTerm termUniqueness
## GO:1901615 organic hydroxy compound metabolic process 0.9524041
## GO:0051301 cell division 0.9830094
## GO:0021700 developmental maturation 0.9493797
## GO:0009987 cellular process 0.9676917
## GO:0007155 cell adhesion 0.9844586
## GO:0006790 sulfur compound metabolic process 0.9335226
## termUniquenessWithinCluster termDispensability
## GO:1901615 1 0
## GO:0051301 1 0
## GO:0021700 1 0
## GO:0009987 1 0
## GO:0007155 1 0
## GO:0006790 1 0#keep only the goterms from the reduced list
go_results <- go_results%>%
filter(GOterm %in% reducedTerms$go)
#add in parent terms to list of go terms
go_results$ParentTerm <- reducedTerms$parentTerm[match(go_results$GOterm, reducedTerms$go)]
go_results <- go_results %>% mutate(Factor = "Up")
head(go_results)## X GOterm over_represented_pvalue under_represented_pvalue numDEInCat
## 1 1 GO:0000122 0 1 16
## 2 3 GO:0000280 0 1 14
## 3 7 GO:0000904 0 1 16
## 4 8 GO:0001101 0 1 13
## 5 9 GO:0001505 0 1 11
## 6 17 GO:0001933 0 1 12
## numInCat term ontology
## 1 16 negative regulation of transcription by RNA polymerase II BP
## 2 14 nuclear division BP
## 3 16 cell morphogenesis involved in differentiation BP
## 4 13 response to acid chemical BP
## 5 11 regulation of neurotransmitter levels BP
## 6 12 negative regulation of protein phosphorylation BP
## bh_adjust ParentTerm Factor
## 1 0 negative regulation of transcription by RNA polymerase II Up
## 2 0 cellular component disassembly Up
## 3 0 post-embryonic animal organ morphogenesis Up
## 4 0 response to acid chemical Up
## 5 0 regulation of neurotransmitter levels Up
## 6 0 purine ribonucleotide metabolic process Upwrite.csv(go_results, "../../../output/WGCNA/goseq_pattern_calcification_filtered.csv")#plot significantly enriched GO terms by Slim Category faceted by slim term
GO.plot_calcification <- ggplot(go_results, aes(x = ontology, y = term)) +
geom_point(aes(size=bh_adjust)) +
scale_size(name="Over rep. p-value", trans="reverse", range=c(1,3))+
facet_grid(ParentTerm ~ ., scales = "free", labeller = label_wrap_gen(width = 5, multi_line = TRUE))+
theme_bw() + theme(panel.border = element_blank(), panel.grid.major = element_blank(),
panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"),
strip.text.y = element_text(angle=0, size = 10),
strip.text.x = element_text(size = 20),
axis.text = element_text(size = 8),
axis.title.x = element_blank(),
axis.title.y = element_blank())
GO.plot_calcification
#Calcification - downregulation (GO terms associated with WGCNA modules demonstrating negative expression in net calcification
### Generate vector with names of all genes
ALL.vector <- c(geneInfo$gene_id)### Generate length vector for all genes
LENGTH.vector <- as.integer(geneInfo$Length)### Generate vector with names in just the module we are analyzing
ID.vector <- geneInfo%>%
filter(moduleColor==c("black","red"))%>%
#get_rows(.data[[module]]))%>%
pull(gene_id)
##Get a list of GO Terms for each module
GO.terms <- geneInfo%>%
filter(moduleColor==c("black","red"))%>%
#filter(get_rows(.data[[module]]))%>%
dplyr::select(GO.terms,gene_id)
head(GO.terms)## GO.terms
## 1 <NA>
## 2 GO:0000226,GO:0001534,GO:0001578,GO:0003341,GO:0003674,GO:0005488,GO:0005515,GO:0005575,GO:0005622,GO:0005623,GO:0005634,GO:0005654,GO:0005730,GO:0005737,GO:0005856,GO:0005875,GO:0005929,GO:0005930,GO:0006928,GO:0006996,GO:0007010,GO:0007017,GO:0007018,GO:0008017,GO:0008092,GO:0008150,GO:0009987,GO:0015630,GO:0015631,GO:0016043,GO:0022607,GO:0030030,GO:0030031,GO:0031514,GO:0031974,GO:0031981,GO:0032838,GO:0032991,GO:0035082,GO:0042995,GO:0043226,GO:0043227,GO:0043228,GO:0043229,GO:0043231,GO:0043232,GO:0043233,GO:0044085,GO:0044422,GO:0044424,GO:0044428,GO:0044430,GO:0044441,GO:0044444,GO:0044446,GO:0044447,GO:0044463,GO:0044464,GO:0044782,GO:0060271,GO:0070013,GO:0070925,GO:0071840,GO:0097014,GO:0099568,GO:0120025,GO:0120031,GO:0120036,GO:0120038
## 3 <NA>
## 4 GO:0000003,GO:0000165,GO:0000166,GO:0000186,GO:0000187,GO:0000902,GO:0000904,GO:0001505,GO:0001558,GO:0001666,GO:0001700,GO:0001726,GO:0001763,GO:0001882,GO:0001883,GO:0001932,GO:0001933,GO:0001934,GO:0002009,GO:0002119,GO:0002164,GO:0002165,GO:0002218,GO:0002220,GO:0002223,GO:0002252,GO:0002253,GO:0002376,GO:0002429,GO:0002431,GO:0002433,GO:0002682,GO:0002684,GO:0002694,GO:0002696,GO:0002757,GO:0002758,GO:0002764,GO:0002768,GO:0003006,GO:0003008,GO:0003012,GO:0003300,GO:0003674,GO:0003824,GO:0004672,GO:0004674,GO:0004708,GO:0004709,GO:0004712,GO:0005488,GO:0005515,GO:0005518,GO:0005525,GO:0005575,GO:0005622,GO:0005623,GO:0005634,GO:0005635,GO:0005654,GO:0005737,GO:0005768,GO:0005829,GO:0005856,GO:0005886,GO:0005911,GO:0005912,GO:0005924,GO:0005925,GO:0006464,GO:0006468,GO:0006469,GO:0006793,GO:0006796,GO:0006807,GO:0006810,GO:0006811,GO:0006820,GO:0006835,GO:0006836,GO:0006865,GO:0006897,GO:0006909,GO:0006915,GO:0006928,GO:0006935,GO:0006950,GO:0006996,GO:0007010,GO:0007043,GO:0007044,GO:0007154,GO:0007155,GO:0007163,GO:0007165,GO:0007166,GO:0007167,GO:0007169,GO:0007254,GO:0007264,GO:0007265,GO:0007266,GO:0007267,GO:0007268,GO:0007269,GO:0007275,GO:0007346,GO:0007391,GO:0007395,GO:0007399,GO:0007409,GO:0007411,GO:0007417,GO:0007420,GO:0007431,GO:0007435,GO:0007444,GO:0007478,GO:0007480,GO:0007528,GO:0007548,GO:0007552,GO:0007560,GO:0007610,GO:0007611,GO:0007612,GO:0008045,GO:0008047,GO:0008064,GO:0008104,GO:0008150,GO:0008152,GO:0008219,GO:0008284,GO:0008285,GO:0008361,GO:0008406,GO:0008582,GO:0009605,GO:0009611,GO:0009628,GO:0009653,GO:0009719,GO:0009725,GO:0009790,GO:0009791,GO:0009792,GO:0009886,GO:0009887,GO:0009888,GO:0009889,GO:0009891,GO:0009892,GO:0009893,GO:0009966,GO:0009967,GO:0009987,GO:0010033,GO:0010171,GO:0010172,GO:0010243,GO:0010466,GO:0010468,GO:0010556,GO:0010557,GO:0010562,GO:0010563,GO:0010604,GO:0010605,GO:0010611,GO:0010614,GO:0010623,GO:0010638,GO:0010646,GO:0010647,GO:0010720,GO:0010721,GO:0010762,GO:0010763,GO:0010769,GO:0010770,GO:0010827,GO:0010828,GO:0010941,GO:0010942,GO:0010951,GO:0010975,GO:0010976,GO:0012501,GO:0012502,GO:0012505,GO:0014047,GO:0014051,GO:0014069,GO:0014070,GO:0014704,GO:0014741,GO:0014743,GO:0014896,GO:0014897,GO:0014910,GO:0014911,GO:0015711,GO:0015718,GO:0015800,GO:0015812,GO:0015849,GO:0016020,GO:0016021,GO:0016032,GO:0016043,GO:0016192,GO:0016202,GO:0016301,GO:0016310,GO:0016328,GO:0016331,GO:0016358,GO:0016477,GO:0016601,GO:0016740,GO:0016772,GO:0016773,GO:0017016,GO:0017048,GO:0017076,GO:0017124,GO:0018105,GO:0018193,GO:0018209,GO:0019001,GO:0019207,GO:0019209,GO:0019219,GO:0019220,GO:0019221,GO:0019222,GO:0019538,GO:0019887,GO:0019899,GO:0019900,GO:0019901,GO:0019904,GO:0019991,GO:0021549,GO:0021761,GO:0021764,GO:0022008,GO:0022037,GO:0022407,GO:0022409,GO:0022414,GO:0022603,GO:0022604,GO:0022607,GO:0022610,GO:0022612,GO:0023014,GO:0023051,GO:0023052,GO:0023056,GO:0023061,GO:0030010,GO:0030016,GO:0030017,GO:0030018,GO:0030027,GO:0030029,GO:0030030,GO:0030036,GO:0030054,GO:0030055,GO:0030056,GO:0030141,GO:0030154,GO:0030155,GO:0030162,GO:0030182,GO:0030234,GO:0030295,GO:0030296,GO:0030307,GO:0030308,GO:0030334,GO:0030335,GO:0030424,GO:0030425,GO:0030426,GO:0030427,GO:0030516,GO:0030832,GO:0030833,GO:0030900,GO:0030902,GO:0031090,GO:0031098,GO:0031110,GO:0031112,GO:0031113,GO:0031116,GO:0031175,GO:0031224,GO:0031252,GO:0031267,GO:0031294,GO:0031295,GO:0031323,GO:0031324,GO:0031325,GO:0031326,GO:0031328,GO:0031334,GO:0031344,GO:0031346,GO:0031347,GO:0031349,GO:0031399,GO:0031400,GO:0031401,GO:0031410,GO:0031532,GO:0031581,GO:0031594,GO:0031674,GO:0031965,GO:0031967,GO:0031974,GO:0031975,GO:0031981,GO:0031982,GO:0032147,GO:0032231,GO:0032233,GO:0032268,GO:0032269,GO:0032270,GO:0032271,GO:0032273,GO:0032279,GO:0032386,GO:0032388,GO:0032501,GO:0032502,GO:0032535,GO:0032549,GO:0032550,GO:0032553,GO:0032555,GO:0032561,GO:0032868,GO:0032869,GO:0032870,GO:0032872,GO:0032874,GO:0032879,GO:0032880,GO:0032886,GO:0032940,GO:0032956,GO:0032970,GO:0032989,GO:0032990,GO:0032991,GO:0033036,GO:0033043,GO:0033135,GO:0033138,GO:0033143,GO:0033145,GO:0033146,GO:0033148,GO:0033157,GO:0033267,GO:0033554,GO:0033673,GO:0033674,GO:0033993,GO:0034097,GO:0034329,GO:0034330,GO:0034613,GO:0034762,GO:0034764,GO:0035070,GO:0035071,GO:0035072,GO:0035075,GO:0035078,GO:0035081,GO:0035107,GO:0035114,GO:0035120,GO:0035218,GO:0035239,GO:0035249,GO:0035262,GO:0035272,GO:0035295,GO:0035556,GO:0035639,GO:0035722,GO:0036094,GO:0036211,GO:0036293,GO:0036314,GO:0036477,GO:0038093,GO:0038094,GO:0038095,GO:0038096,GO:0040008,GO:0040011,GO:0040012,GO:0040017,GO:0040039,GO:0042060,GO:0042127,GO:0042221,GO:0042325,GO:0042326,GO:0042327,GO:0042330,GO:0042802,GO:0042981,GO:0042995,GO:0043005,GO:0043025,GO:0043065,GO:0043066,GO:0043067,GO:0043068,GO:0043069,GO:0043085,GO:0043086,GO:0043113,GO:0043154,GO:0043167,GO:0043168,GO:0043170,GO:0043226,GO:0043227,GO:0043228,GO:0043229,GO:0043231,GO:0043232,GO:0043233,GO:0043254,GO:0043281,GO:0043292,GO:0043297,GO:0043405,GO:0043406,GO:0043408,GO:0043410,GO:0043412,GO:0043434,GO:0043502,GO:0043506,GO:0043507,GO:0043523,GO:0043525,GO:0043549,GO:0044057,GO:0044085,GO:0044087,GO:0044089,GO:0044092,GO:0044093,GO:0044237,GO:0044238,GO:0044260,GO:0044267,GO:0044291,GO:0044297,GO:0044403,GO:0044419,GO:0044422,GO:0044424,GO:0044425,GO:0044428,GO:0044444,GO:0044446,GO:0044449,GO:0044456,GO:0044459,GO:0044463,GO:0044464,GO:0044877,GO:0045088,GO:0045089,GO:0045137,GO:0045202,GO:0045216,GO:0045595,GO:0045596,GO:0045597,GO:0045664,GO:0045666,GO:0045773,GO:0045785,GO:0045843,GO:0045859,GO:0045860,GO:0045861,GO:0045887,GO:0045926,GO:0045927,GO:0045935,GO:0045936,GO:0045937,GO:0046324,GO:0046326,GO:0046328,GO:0046330,GO:0046620,GO:0046621,GO:0046717,GO:0046777,GO:0046903,GO:0046942,GO:0048010,GO:0048012,GO:0048013,GO:0048102,GO:0048167,GO:0048365,GO:0048468,GO:0048471,GO:0048513,GO:0048518,GO:0048519,GO:0048522,GO:0048523,GO:0048563,GO:0048569,GO:0048583,GO:0048584,GO:0048598,GO:0048608,GO:0048634,GO:0048635,GO:0048638,GO:0048639,GO:0048640,GO:0048660,GO:0048661,GO:0048666,GO:0048667,GO:0048699,GO:0048707,GO:0048729,GO:0048731,GO:0048732,GO:0048736,GO:0048737,GO:0048754,GO:0048812,GO:0048813,GO:0048814,GO:0048856,GO:0048858,GO:0048869,GO:0048870,GO:0050690,GO:0050730,GO:0050731,GO:0050767,GO:0050769,GO:0050770,GO:0050772,GO:0050773,GO:0050775,GO:0050776,GO:0050778,GO:0050789,GO:0050790,GO:0050793,GO:0050794,GO:0050803,GO:0050804,GO:0050807,GO:0050808,GO:0050851,GO:0050852,GO:0050863,GO:0050865,GO:0050867,GO:0050870,GO:0050877,GO:0050890,GO:0050896,GO:0051020,GO:0051049,GO:0051050,GO:0051052,GO:0051054,GO:0051093,GO:0051094,GO:0051128,GO:0051130,GO:0051147,GO:0051148,GO:0051153,GO:0051154,GO:0051171,GO:0051172,GO:0051173,GO:0051174,GO:0051179,GO:0051222,GO:0051223,GO:0051234,GO:0051239,GO:0051240,GO:0051241,GO:0051246,GO:0051247,GO:0051248,GO:0051249,GO:0051251,GO:0051270,GO:0051272,GO:0051336,GO:0051338,GO:0051346,GO:0051347,GO:0051348,GO:0051403,GO:0051492,GO:0051493,GO:0051495,GO:0051496,GO:0051641,GO:0051649,GO:0051668,GO:0051674,GO:0051704,GO:0051716,GO:0051726,GO:0051932,GO:0051960,GO:0051962,GO:0051963,GO:0051965,GO:0052547,GO:0052548,GO:0055021,GO:0055022,GO:0055024,GO:0055026,GO:0060033,GO:0060242,GO:0060244,GO:0060255,GO:0060284,GO:0060322,GO:0060341,GO:0060420,GO:0060429,GO:0060548,GO:0060562,GO:0060996,GO:0060997,GO:0060998,GO:0060999,GO:0061001,GO:0061003,GO:0061050,GO:0061052,GO:0061097,GO:0061098,GO:0061117,GO:0061138,GO:0061387,GO:0061458,GO:0061534,GO:0061535,GO:0061564,GO:0065007,GO:0065008,GO:0065009,GO:0070013,GO:0070161,GO:0070201,GO:0070302,GO:0070304,GO:0070482,GO:0070507,GO:0070671,GO:0070727,GO:0070848,GO:0070887,GO:0071310,GO:0071345,GO:0071349,GO:0071363,GO:0071375,GO:0071407,GO:0071417,GO:0071437,GO:0071495,GO:0071559,GO:0071560,GO:0071702,GO:0071704,GO:0071705,GO:0071840,GO:0071900,GO:0071902,GO:0071944,GO:0072657,GO:0080090,GO:0080134,GO:0080135,GO:0090066,GO:0090087,GO:0090257,GO:0090313,GO:0090314,GO:0090316,GO:0097061,GO:0097159,GO:0097194,GO:0097305,GO:0097367,GO:0097447,GO:0097458,GO:0097482,GO:0097485,GO:0097708,GO:0098597,GO:0098657,GO:0098772,GO:0098794,GO:0098916,GO:0098975,GO:0098984,GO:0099080,GO:0099081,GO:0099173,GO:0099175,GO:0099177,GO:0099503,GO:0099512,GO:0099536,GO:0099537,GO:0099572,GO:0099643,GO:0106027,GO:0110020,GO:0110053,GO:0120025,GO:0120035,GO:0120036,GO:0120038,GO:0120039,GO:0140096,GO:0150034,GO:1900006,GO:1900076,GO:1900078,GO:1900117,GO:1900118,GO:1900271,GO:1901214,GO:1901216,GO:1901265,GO:1901363,GO:1901564,GO:1901652,GO:1901653,GO:1901654,GO:1901698,GO:1901699,GO:1901700,GO:1901701,GO:1901861,GO:1901862,GO:1902531,GO:1902533,GO:1902903,GO:1902905,GO:1903037,GO:1903039,GO:1903533,GO:1903827,GO:1903829,GO:1904396,GO:1904398,GO:1904705,GO:1904707,GO:1904752,GO:1904754,GO:1904951,GO:1905207,GO:1905208,GO:1905475,GO:1905477,GO:2000026,GO:2000112,GO:2000116,GO:2000117,GO:2000145,GO:2000147,GO:2000278,GO:2000573,GO:2000725,GO:2000726,GO:2001233,GO:2001235,GO:2001236,GO:2001238,GO:2001270,GO:2001271,GO:2001273,GO:2001275
## 5 GO:0003674,GO:0003824,GO:0004335,GO:0005575,GO:0005576,GO:0005615,GO:0005622,GO:0005623,GO:0005737,GO:0005975,GO:0005996,GO:0006012,GO:0006793,GO:0006796,GO:0008150,GO:0008152,GO:0009987,GO:0016020,GO:0016301,GO:0016310,GO:0016740,GO:0016772,GO:0016773,GO:0019200,GO:0019318,GO:0031982,GO:0043226,GO:0043227,GO:0043230,GO:0044237,GO:0044238,GO:0044262,GO:0044281,GO:0044421,GO:0044424,GO:0044464,GO:0046835,GO:0070062,GO:0071704,GO:1903561
## 6 -
## gene_id
## 1 Pocillopora_acuta_HIv2___RNAseq.11750_t
## 2 Pocillopora_acuta_HIv2___RNAseq.14688_t
## 3 Pocillopora_acuta_HIv2___RNAseq.15878_t
## 4 Pocillopora_acuta_HIv2___RNAseq.16174_t
## 5 Pocillopora_acuta_HIv2___RNAseq.16779_t
## 6 Pocillopora_acuta_HIv2___RNAseq.21443_t##Format to have one goterm per row with gene ID repeated
split <- strsplit(as.character(GO.terms$GO.terms), ",")
split2 <- data.frame(v1 = rep.int(GO.terms$gene, sapply(split, length)), v2 = unlist(split))
colnames(split2) <- c("gene", "GO.terms")
GO.terms <- split2##Construct list of genes with 1 for genes in module and 0 for genes not in the module
gene.vector=as.integer(ALL.vector %in% ID.vector)
names(gene.vector) <- ALL.vector#set names
#weight gene vector by bias for length of gene
pwf <- nullp(gene.vector, ID.vector, bias.data=LENGTH.vector) ## Warning in pcls(G): initial point very close to some inequality constraints
#run goseq using Wallenius method for all categories of GO terms
GO.wall<-goseq(pwf, ID.vector, gene2cat=GO.terms, test.cats=c("GO:BP", "GO:MF", "GO:CC"), method="Wallenius", use_genes_without_cat=TRUE)## Using manually entered categories.## Calculating the p-values...## 'select()' returned 1:1 mapping between keys and columnsGO <- GO.wall[order(GO.wall$over_represented_pvalue),]
colnames(GO)[1] <- "GOterm"#adjust p-values
GO$bh_adjust <- p.adjust(GO$over_represented_pvalue, method="BH") #add adjusted p-values#Filtering for p < 0.01
GO <- GO %>%
dplyr::filter(bh_adjust<0.00001) %>%
dplyr::arrange(., ontology, bh_adjust)
#Write file of results
write.csv(GO, file = "../../../output/WGCNA/goseq_pattern_calcification_down.csv")module_vector <- c(levels(geneInfo$moduleColor))
ontologies <- c("BP", "MF")go_results <- read.csv("../../../output/WGCNA/goseq_pattern_calcification_down.csv")go_results<-go_results%>%
filter(ontology=="BP")%>%
filter(bh_adjust != "NA") %>%
filter(numInCat>10)%>%
arrange(., bh_adjust)
head(go_results)## X GOterm over_represented_pvalue under_represented_pvalue numDEInCat
## 1 1 GO:0000122 0 1 16
## 2 2 GO:0000165 0 1 11
## 3 3 GO:0000375 0 1 11
## 4 7 GO:0001505 0 1 15
## 5 10 GO:0001666 0 1 14
## 6 16 GO:0001933 0 1 15
## numInCat term ontology
## 1 16 negative regulation of transcription by RNA polymerase II BP
## 2 11 MAPK cascade BP
## 3 11 RNA splicing, via transesterification reactions BP
## 4 15 regulation of neurotransmitter levels BP
## 5 14 response to hypoxia BP
## 6 15 negative regulation of protein phosphorylation BP
## bh_adjust
## 1 0
## 2 0
## 3 0
## 4 0
## 5 0
## 6 0library(rrvgo)
#Reduce/collapse GO term set with the rrvgo package
simMatrix <- calculateSimMatrix(go_results$GOterm,
orgdb="org.Ce.eg.db", #c. elegans database
ont="BP",
method="Rel")## preparing gene to GO mapping data...## preparing IC data... #calculate similarity
scores <- setNames(-log(go_results$bh_adjust), go_results$GOterm)
reducedTerms <- reduceSimMatrix(simMatrix,
scores,
threshold=0.7,
orgdb="org.Ce.eg.db")
head(reducedTerms)## go cluster parent score size
## GO:0009987 GO:0009987 31 GO:0009987 Inf 0
## GO:0007568 GO:0007568 24 GO:0007568 Inf 19
## GO:0007163 GO:0007163 21 GO:0007163 Inf 27
## GO:0005975 GO:0005975 12 GO:0005975 Inf 161
## GO:0051606 GO:0051606 51 GO:0051606 Inf 0
## GO:0040029 GO:0040029 32 GO:0040029 Inf 7
## term
## GO:0009987 cellular process
## GO:0007568 aging
## GO:0007163 establishment or maintenance of cell polarity
## GO:0005975 carbohydrate metabolic process
## GO:0051606 detection of stimulus
## GO:0040029 epigenetic regulation of gene expression
## parentTerm termUniqueness
## GO:0009987 cellular process 0.9686151
## GO:0007568 aging 0.9529381
## GO:0007163 establishment or maintenance of cell polarity 0.9847182
## GO:0005975 carbohydrate metabolic process 0.9516632
## GO:0051606 detection of stimulus 0.9578557
## GO:0040029 epigenetic regulation of gene expression 0.8377148
## termUniquenessWithinCluster termDispensability
## GO:0009987 1.0000000 0
## GO:0007568 1.0000000 0
## GO:0007163 1.0000000 0
## GO:0005975 1.0000000 0
## GO:0051606 0.7015000 0
## GO:0040029 0.6341818 0#keep only the goterms from the reduced list
go_results<-go_results%>%
filter(GOterm %in% reducedTerms$go)
#add in parent terms to list of go terms
go_results$ParentTerm<-reducedTerms$parentTerm[match(go_results$GOterm, reducedTerms$go)]
go_results <- go_results %>% mutate(Factor = "Down")
head(go_results)## X GOterm over_represented_pvalue under_represented_pvalue numDEInCat
## 1 1 GO:0000122 0 1 16
## 2 2 GO:0000165 0 1 11
## 3 3 GO:0000375 0 1 11
## 4 7 GO:0001505 0 1 15
## 5 10 GO:0001666 0 1 14
## 6 16 GO:0001933 0 1 15
## numInCat term ontology
## 1 16 negative regulation of transcription by RNA polymerase II BP
## 2 11 MAPK cascade BP
## 3 11 RNA splicing, via transesterification reactions BP
## 4 15 regulation of neurotransmitter levels BP
## 5 14 response to hypoxia BP
## 6 15 negative regulation of protein phosphorylation BP
## bh_adjust ParentTerm
## 1 0 negative regulation of transcription by RNA polymerase II
## 2 0 transmembrane receptor protein tyrosine kinase signaling pathway
## 3 0 purine-containing compound metabolic process
## 4 0 regulation of hormone levels
## 5 0 response to ionizing radiation
## 6 0 purine ribonucleotide metabolic process
## Factor
## 1 Down
## 2 Down
## 3 Down
## 4 Down
## 5 Down
## 6 Downwrite.csv(go_results, "../../../output/WGCNA/goseq_pattern_calcification_down_filtered.csv")#plot significantly enriched GO terms by Slim Category faceted by slim term
GO.plot_calcification_down <- ggplot(go_results, aes(x = ontology, y = term)) +
geom_point(aes(size=bh_adjust)) +
scale_size(name="Over rep. p-value", trans="reverse", range=c(1,3))+
facet_grid(ParentTerm ~ ., scales = "free", labeller = label_wrap_gen(width = 5, multi_line = TRUE))+
theme_bw() + theme(panel.border = element_blank(), panel.grid.major = element_blank(),
panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"),
strip.text.y = element_text(angle=0, size = 10),
strip.text.x = element_text(size = 20),
axis.text = element_text(size = 8),
axis.title.x = element_blank(),
axis.title.y = element_blank())
GO.plot_calcification_down
#Frequency of GO terms
cal_up_terms <-read.csv("../../../output/WGCNA/goseq_pattern_calcification_filtered.csv")
cal_down_terms <-read.csv("../../../output/WGCNA/goseq_pattern_calcification_down_filtered.csv")cal_biomin_terms <-read.csv("../../../output/Biomineralization_goterms.csv")
head(cal_biomin_terms)## Factor X.1 X GOterm over_represented_pvalue under_represented_pvalue
## 1 Biomin 110 158 GO:0030048 1 0.9417955
## 2 Biomin 135 192 GO:0070252 1 0.9417955
## 3 Biomin 397 563 GO:0006928 1 0.8194394
## 4 Biomin 449 627 GO:0030334 1 0.9494130
## 5 Biomin 450 628 GO:0030335 1 0.9494130
## 6 Biomin 451 629 GO:0030336 1 0.9494130
## numDEInCat numInCat term ontology
## 1 0 1 actin filament-based movement BP
## 2 0 1 actin-mediated cell contraction BP
## 3 0 4 movement of cell or subcellular component BP
## 4 0 1 regulation of cell migration BP
## 5 0 1 positive regulation of cell migration BP
## 6 0 1 negative regulation of cell migration BP
## bh_adjust ParentTerm
## 1 1 actin-mediated cell contraction
## 2 1 actin-mediated cell contraction
## 3 1 actin-mediated cell contraction
## 4 1 actin-mediated cell contraction
## 5 1 actin-mediated cell contraction
## 6 1 actin-mediated cell contractionhead(cal_up_terms)## X.1 X GOterm over_represented_pvalue under_represented_pvalue numDEInCat
## 1 1 1 GO:0000122 0 1 16
## 2 2 3 GO:0000280 0 1 14
## 3 3 7 GO:0000904 0 1 16
## 4 4 8 GO:0001101 0 1 13
## 5 5 9 GO:0001505 0 1 11
## 6 6 17 GO:0001933 0 1 12
## numInCat term ontology
## 1 16 negative regulation of transcription by RNA polymerase II BP
## 2 14 nuclear division BP
## 3 16 cell morphogenesis involved in differentiation BP
## 4 13 response to acid chemical BP
## 5 11 regulation of neurotransmitter levels BP
## 6 12 negative regulation of protein phosphorylation BP
## bh_adjust ParentTerm Factor
## 1 0 negative regulation of transcription by RNA polymerase II Up
## 2 0 cellular component disassembly Up
## 3 0 post-embryonic animal organ morphogenesis Up
## 4 0 response to acid chemical Up
## 5 0 regulation of neurotransmitter levels Up
## 6 0 purine ribonucleotide metabolic process Uphead(cal_down_terms)## X.1 X GOterm over_represented_pvalue under_represented_pvalue numDEInCat
## 1 1 1 GO:0000122 0 1 16
## 2 2 2 GO:0000165 0 1 11
## 3 3 3 GO:0000375 0 1 11
## 4 4 7 GO:0001505 0 1 15
## 5 5 10 GO:0001666 0 1 14
## 6 6 16 GO:0001933 0 1 15
## numInCat term ontology
## 1 16 negative regulation of transcription by RNA polymerase II BP
## 2 11 MAPK cascade BP
## 3 11 RNA splicing, via transesterification reactions BP
## 4 15 regulation of neurotransmitter levels BP
## 5 14 response to hypoxia BP
## 6 15 negative regulation of protein phosphorylation BP
## bh_adjust ParentTerm
## 1 0 negative regulation of transcription by RNA polymerase II
## 2 0 transmembrane receptor protein tyrosine kinase signaling pathway
## 3 0 purine-containing compound metabolic process
## 4 0 regulation of hormone levels
## 5 0 response to ionizing radiation
## 6 0 purine ribonucleotide metabolic process
## Factor
## 1 Down
## 2 Down
## 3 Down
## 4 Down
## 5 Down
## 6 Downall_terms<- merge(cal_up_terms,cal_down_terms, by=c("Factor","GOterm","X.1","X","GOterm","over_represented_pvalue","under_represented_pvalue","numDEInCat","numInCat","term","ontology","bh_adjust","ParentTerm"),all=T)
all_terms<- merge(all_terms,cal_biomin_terms, by=c("Factor","GOterm","X.1","X","GOterm","over_represented_pvalue","under_represented_pvalue","numDEInCat","numInCat","term","ontology","bh_adjust","ParentTerm"),all=T)
all_terms$GOterm<-as.factor(all_terms$GOterm)
head(all_terms)## Factor GOterm X.1 X over_represented_pvalue under_represented_pvalue
## 1 Biomin GO:0000003 748 1054 1 0.7918886
## 2 Biomin GO:0000041 335 479 1 0.9545025
## 3 Biomin GO:0000122 295 438 1 0.9689632
## 4 Biomin GO:0000132 97 143 1 0.9417955
## 5 Biomin GO:0000226 390 556 1 0.8588726
## 6 Biomin GO:0000278 595 812 1 0.9325796
## numDEInCat numInCat term
## 1 0 5 reproduction
## 2 0 1 transition metal ion transport
## 3 0 1 negative regulation of transcription by RNA polymerase II
## 4 0 1 establishment of mitotic spindle orientation
## 5 0 3 microtubule cytoskeleton organization
## 6 0 2 mitotic cell cycle
## ontology bh_adjust
## 1 BP 1
## 2 BP 1
## 3 BP 1
## 4 BP 1
## 5 BP 1
## 6 BP 1
## ParentTerm
## 1 gonad development
## 2 divalent metal ion transport
## 3 negative regulation of nucleobase-containing compound metabolic process
## 4 establishment of mitotic spindle orientation
## 5 microtubule-based process
## 6 microtubule cytoskeleton organization involved in mitosisall_terms_merged <- all_terms %>%
group_by(GOterm) %>%
dplyr::summarise(
ParentTerm = paste(unique(ParentTerm), collapse = ", "),
Factor = paste(unique(Factor), collapse = ", ")
)
head(all_terms_merged)## # A tibble: 6 × 3
## GOterm ParentTerm Factor
## <fct> <chr> <chr>
## 1 GO:0000003 gonad development, development of primary sexual characteri… Biomi…
## 2 GO:0000041 divalent metal ion transport Biomin
## 3 GO:0000122 negative regulation of nucleobase-containing compound metab… Biomi…
## 4 GO:0000132 establishment of mitotic spindle orientation Biomin
## 5 GO:0000165 transmembrane receptor protein tyrosine kinase signaling pa… Down
## 6 GO:0000226 microtubule-based process, regulation of microtubule-based … Biomi…write.csv(all_terms_merged, "../../../output/WGCNA/Merged_GOterms_Factor_ParentTerm.csv")cal_freq_terms <-read.csv("../../../output/WGCNA/goseq_pattern_calcification_all.csv")
head(cal_freq_terms)## ParentTerm Calcification.direction
## 1 negative regulation of organelle organization Up
## 2 negative regulation of protein modification process Up
## 3 anion transport Up
## 4 sensory organ morphogenesis Up
## 5 cytokine-mediated signaling pathway Up
## 6 biological regulation Up
## Number.of.terms Frequency.of.shared.biomin.GOterms
## 1 39 12
## 2 26 11
## 3 23 6
## 4 21 3
## 5 20 2
## 6 19 9
## Proportion.of.shared.GO.terms.with.biomineralization.genes
## 1 0.3076923
## 2 0.4230769
## 3 0.2608696
## 4 0.1428571
## 5 0.1000000
## 6 0.4736842
## Percentage.of.shared.GO.terms.with.biomineralization.genes
## 1 30.76923
## 2 42.30769
## 3 26.08696
## 4 14.28571
## 5 10.00000
## 6 47.36842##Frequency >10 GO terms upregulation
cal_freq_terms_filtered_up <- cal_freq_terms %>%
filter(Number.of.terms>=10) %>%
filter(Calcification.direction=="Up")###Figure
#counts$Direction.of.flat.origin<- factor(counts$Direction.of.flat.origin, levels =c("up","no pattern","down"))
#counts$Module<- factor(counts$Module, levels=c("Blue","Brown","Greenyellow","Cyan","Pink","Magenta","Lightcyan","Midnight blue","Purple","Turquiose","Red","Black"))
freq_fig_up<-ggplot(cal_freq_terms_filtered_up, aes(y=Number.of.terms,x=reorder(ParentTerm, Number.of.terms), fill=Percentage.of.shared.GO.terms.with.biomineralization.genes,group=1))+
#facet_wrap(~Calcification.direction, nrow = 1)+
geom_point(size=5, alpha=1, pch=21,color="black")+
geom_segment(aes(x=ParentTerm, xend=ParentTerm, y=0, yend=Number.of.terms)) +
geom_hline(yintercept = 0, linetype="solid", color = 'black', size=0.5, show.legend = TRUE)+
coord_flip()+
scale_y_continuous(expression(GO~term~counts),limits=c(0,40))+
#scale_color_manual("Direction.of.flat.origin",values= c("up"="#b2182b","no pattern"="grey","down" ="#67a9cf"))+
#scale_fill_manual("Direction.of.flat.origin",values= c("up"="#b2182b","no pattern"="grey","down" ="#67a9cf"))+
scale_fill_gradientn(colours=c("white","#fddbc7","#f4a582","#d6604d","#b2182b"), na.value = "grey98",limits = c(0, 100))+
#scale_color_gradientn(colours=c("#b2182b","#fddbc7","white","#d1e5f0","#67a9cf", "#67a9cf", "#2166ac"), na.value = "grey98",limits = c(-0, 40))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, hjust=0.95,size=12),
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),
panel.background= element_rect(fill=NA, color='black'),
legend.title = element_blank(),
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_blank(),
strip.text = element_text(size=12))#making the axis title larger ## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.freq_fig_up
##Frequency >10 GO terms downregulation
cal_freq_terms_filtered_down <- cal_freq_terms %>%
filter(Number.of.terms>=10) %>%
filter(Calcification.direction=="Down")###Figure
freq_fig_down<-ggplot(cal_freq_terms_filtered_down, aes(y=Number.of.terms,x=reorder(ParentTerm, Number.of.terms), fill=Percentage.of.shared.GO.terms.with.biomineralization.genes))+
#facet_wrap(~Calcification.direction, nrow = 1)+
geom_point(size=5, alpha=1, pch=21,color="black")+
geom_segment(aes(x=ParentTerm, xend=ParentTerm, y=0, yend=Number.of.terms)) +
#geom_hline(yintercept = 0, linetype="solid", color = 'black', size=0.5, show.legend = TRUE)+
coord_flip()+
scale_y_continuous(expression(GO~term~counts),limits=c(0,40))+
#scale_color_manual("Direction.of.flat.origin",values= c("up"="#b2182b","no pattern"="grey","down" ="#67a9cf"))+
#scale_fill_manual("Direction.of.flat.origin",values= c("up"="#b2182b","no pattern"="grey","down" ="#67a9cf"))+
scale_fill_gradientn(colours=c("white","#d1e5f0","#92c5de","#4393c3","#2166ac"), na.value = "grey98",limits = c(0, 100))+
#scale_fill_gradientn(colours=c("#fddbc7","#f4a582","#d6604d","#b2182b"), na.value = "grey98",limits = c(10, 40))+
#scale_color_gradientn(colours=c("#b2182b","#fddbc7","white","#d1e5f0","#67a9cf", "#67a9cf", "#2166ac"), na.value = "grey98",limits = c(-0, 40))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, hjust=0.95, size=12),
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),
panel.background= element_rect(fill=NA, color='black'),
legend.title = element_blank(),
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_blank(),
strip.text = element_text(size=12))#making the axis title larger
freq_fig_down
compare_figs<-cowplot::plot_grid(freq_fig_up, freq_fig_down, nrow=2, align="v")
compare_figs
##Frequency all GO terms upregulation
cal_freq_terms_filtered_up_all <- cal_freq_terms %>%
filter(Calcification.direction=="Up")
head(cal_freq_terms_filtered_up_all)## ParentTerm Calcification.direction
## 1 negative regulation of organelle organization Up
## 2 negative regulation of protein modification process Up
## 3 anion transport Up
## 4 sensory organ morphogenesis Up
## 5 cytokine-mediated signaling pathway Up
## 6 biological regulation Up
## Number.of.terms Frequency.of.shared.biomin.GOterms
## 1 39 12
## 2 26 11
## 3 23 6
## 4 21 3
## 5 20 2
## 6 19 9
## Proportion.of.shared.GO.terms.with.biomineralization.genes
## 1 0.3076923
## 2 0.4230769
## 3 0.2608696
## 4 0.1428571
## 5 0.1000000
## 6 0.4736842
## Percentage.of.shared.GO.terms.with.biomineralization.genes
## 1 30.76923
## 2 42.30769
## 3 26.08696
## 4 14.28571
## 5 10.00000
## 6 47.36842###Figure
#counts$Direction.of.flat.origin<- factor(counts$Direction.of.flat.origin, levels =c("up","no pattern","down"))
#counts$Module<- factor(counts$Module, levels=c("Blue","Brown","Greenyellow","Cyan","Pink","Magenta","Lightcyan","Midnight blue","Purple","Turquiose","Red","Black"))
freq_fig_up<-ggplot(cal_freq_terms_filtered_up_all, aes(y=Number.of.terms,x=reorder(ParentTerm, Number.of.terms), fill=Percentage.of.shared.GO.terms.with.biomineralization.genes,group=1))+
#facet_wrap(~Calcification.direction, nrow = 1)+
geom_point(size=5, alpha=1, pch=21,color="black")+
geom_segment(aes(x=ParentTerm, xend=ParentTerm, y=0, yend=Number.of.terms)) +
geom_hline(yintercept = 0, linetype="solid", color = 'black', size=0.5, show.legend = TRUE)+
coord_flip()+
scale_y_continuous(expression(GO~term~counts),limits=c(0,40))+
#scale_color_manual("Direction.of.flat.origin",values= c("up"="#b2182b","no pattern"="grey","down" ="#67a9cf"))+
#scale_fill_manual("Direction.of.flat.origin",values= c("up"="#b2182b","no pattern"="grey","down" ="#67a9cf"))+
scale_fill_gradientn(colours=c("white","#fddbc7","#f4a582","#d6604d","#b2182b"), na.value = "grey98",limits = c(0, 100))+
#scale_color_gradientn(colours=c("#b2182b","#fddbc7","white","#d1e5f0","#67a9cf", "#67a9cf", "#2166ac"), na.value = "grey98",limits = c(-0, 40))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, hjust=0.95,size=12),
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),
panel.background= element_rect(fill=NA, color='black'),
legend.title = element_blank(),
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_blank(),
strip.text = element_text(size=12))#making the axis title larger
freq_fig_up
##Frequency all GO terms downregulation
cal_freq_terms_filtered_down_all <- cal_freq_terms %>%
filter(Calcification.direction=="Down")
cal_freq_terms_filtered_down_all## ParentTerm
## 1 aging
## 2 axon guidance
## 3 biological regulation
## 4 carbohydrate derivative biosynthetic process
## 5 carbohydrate metabolic process
## 6 cation transport
## 7 cellular lipid metabolic process
## 8 cellular process
## 9 cellular response to abiotic stimulus
## 10 cellular response to external stimulus
## 11 cellular response to hormone stimulus
## 12 detection of stimulus
## 13 development of primary sexual characteristics
## 14 developmental growth
## 15 DNA repair
## 16 drug metabolic process
## 17 embryonic organ development
## 18 establishment or maintenance of cell polarity
## 19 exocytosis
## 20 gastrulation
## 21 head development
## 22 histone modification
## 23 import into cell
## 24 leukocyte activation
## 25 locomotory behavior
## 26 macromolecule metabolic process
## 27 memory
## 28 metabolic process
## 29 morphogenesis of embryonic epithelium
## 30 negative regulation of catabolic process
## 31 negative regulation of cell development
## 32 negative regulation of mitotic cell cycle
## 33 negative regulation of neurogenesis
## 34 negative regulation of transcription by RNA polymerase II
## 35 nucleotide metabolic process
## 36 organonitrogen compound metabolic process
## 37 oxidation-reduction process
## 38 positive regulation of cell motility
## 39 positive regulation of defense response
## 40 positive regulation of immune response
## 41 positive regulation of kinase activity
## 42 positive regulation of multi-organism process
## 43 post-embryonic animal morphogenesis
## 44 protein localization to organelle
## 45 protein modification by small protein conjugation or removal
## 46 purine ribonucleotide metabolic process
## 47 regulation of actin cytoskeleton organization
## 48 regulation of cell population proliferation
## 49 regulation of cell size
## 50 regulation of cell-cell adhesion
## 51 regulation of gene expression, epigenetic
## 52 regulation of ion transport
## 53 regulation of microtubule-based process
## 54 regulation of neuron death
## 55 regulation of peptide secretion
## 56 regulation of Ras protein signal transduction
## 57 response to ionizing radiation
## 58 response to xenobiotic stimulus
## 59 ribose phosphate metabolic process
## 60 rRNA metabolic process
## 61 transcription by RNA polymerase II
## 62 transmembrane receptor protein tyrosine kinase signaling pathway
## 63 tube development
## Calcification.direction Number.of.terms Frequency.of.shared.biomin.GOterms
## 1 Down 12 11
## 2 Down 7 7
## 3 Down 16 9
## 4 Down 2 1
## 5 Down 1 0
## 6 Down 14 14
## 7 Down 3 1
## 8 Down 1 1
## 9 Down 2 0
## 10 Down 5 5
## 11 Down 4 4
## 12 Down 6 3
## 13 Down 10 8
## 14 Down 8 6
## 15 Down 8 5
## 16 Down 1 1
## 17 Down 19 19
## 18 Down 1 1
## 19 Down 9 1
## 20 Down 7 7
## 21 Down 2 2
## 22 Down 39 27
## 23 Down 1 1
## 24 Down 2 0
## 25 Down 2 2
## 26 Down 3 3
## 27 Down 9 5
## 28 Down 6 6
## 29 Down 7 7
## 30 Down 13 12
## 31 Down 10 10
## 32 Down 10 7
## 33 Down 13 11
## 34 Down 17 17
## 35 Down 7 7
## 36 Down 6 4
## 37 Down 1 1
## 38 Down 8 7
## 39 Down 7 4
## 40 Down 9 1
## 41 Down 20 17
## 42 Down 10 6
## 43 Down 19 19
## 44 Down 14 9
## 45 Down 6 4
## 46 Down 13 7
## 47 Down 4 2
## 48 Down 4 1
## 49 Down 20 18
## 50 Down 2 0
## 51 Down 27 26
## 52 Down 17 7
## 53 Down 3 2
## 54 Down 13 5
## 55 Down 8 0
## 56 Down 7 6
## 57 Down 7 5
## 58 Down 25 19
## 59 Down 22 12
## 60 Down 6 1
## 61 Down 14 1
## 62 Down 23 21
## 63 Down 3 3
## Proportion.of.shared.GO.terms.with.biomineralization.genes
## 1 0.91666667
## 2 1.00000000
## 3 0.56250000
## 4 0.50000000
## 5 0.00000000
## 6 1.00000000
## 7 0.33333333
## 8 1.00000000
## 9 0.00000000
## 10 1.00000000
## 11 1.00000000
## 12 0.50000000
## 13 0.80000000
## 14 0.75000000
## 15 0.62500000
## 16 1.00000000
## 17 1.00000000
## 18 1.00000000
## 19 0.11111111
## 20 1.00000000
## 21 1.00000000
## 22 0.69230769
## 23 1.00000000
## 24 0.00000000
## 25 1.00000000
## 26 1.00000000
## 27 0.55555556
## 28 1.00000000
## 29 1.00000000
## 30 0.92307692
## 31 1.00000000
## 32 0.70000000
## 33 0.84615385
## 34 1.00000000
## 35 1.00000000
## 36 0.66666667
## 37 1.00000000
## 38 0.87500000
## 39 0.57142857
## 40 0.11111111
## 41 0.85000000
## 42 0.60000000
## 43 1.00000000
## 44 0.64285714
## 45 0.66666667
## 46 0.53846154
## 47 0.50000000
## 48 0.25000000
## 49 0.90000000
## 50 0.00000000
## 51 0.96296296
## 52 0.41176471
## 53 0.66666667
## 54 0.38461538
## 55 0.00000000
## 56 0.85714286
## 57 0.71428571
## 58 0.76000000
## 59 0.54545455
## 60 0.16666667
## 61 0.07142857
## 62 0.91304348
## 63 1.00000000
## Percentage.of.shared.GO.terms.with.biomineralization.genes
## 1 91.666667
## 2 100.000000
## 3 56.250000
## 4 50.000000
## 5 0.000000
## 6 100.000000
## 7 33.333333
## 8 100.000000
## 9 0.000000
## 10 100.000000
## 11 100.000000
## 12 50.000000
## 13 80.000000
## 14 75.000000
## 15 62.500000
## 16 100.000000
## 17 100.000000
## 18 100.000000
## 19 11.111111
## 20 100.000000
## 21 100.000000
## 22 69.230769
## 23 100.000000
## 24 0.000000
## 25 100.000000
## 26 100.000000
## 27 55.555556
## 28 100.000000
## 29 100.000000
## 30 92.307692
## 31 100.000000
## 32 70.000000
## 33 84.615385
## 34 100.000000
## 35 100.000000
## 36 66.666667
## 37 100.000000
## 38 87.500000
## 39 57.142857
## 40 11.111111
## 41 85.000000
## 42 60.000000
## 43 100.000000
## 44 64.285714
## 45 66.666667
## 46 53.846154
## 47 50.000000
## 48 25.000000
## 49 90.000000
## 50 0.000000
## 51 96.296296
## 52 41.176471
## 53 66.666667
## 54 38.461538
## 55 0.000000
## 56 85.714286
## 57 71.428571
## 58 76.000000
## 59 54.545455
## 60 16.666667
## 61 7.142857
## 62 91.304348
## 63 100.000000###Figure
freq_fig_down<-ggplot(cal_freq_terms_filtered_down_all, aes(y=Number.of.terms,x=reorder(ParentTerm, Number.of.terms), fill=Percentage.of.shared.GO.terms.with.biomineralization.genes))+
#facet_wrap(~Calcification.direction, nrow = 1)+
geom_point(size=5, alpha=1, pch=21,color="black")+
geom_segment(aes(x=ParentTerm, xend=ParentTerm, y=0, yend=Number.of.terms)) +
#geom_hline(yintercept = 0, linetype="solid", color = 'black', size=0.5, show.legend = TRUE)+
coord_flip()+
scale_y_continuous(expression(GO~term~counts),limits=c(0,40))+
#scale_color_manual("Direction.of.flat.origin",values= c("up"="#b2182b","no pattern"="grey","down" ="#67a9cf"))+
#scale_fill_manual("Direction.of.flat.origin",values= c("up"="#b2182b","no pattern"="grey","down" ="#67a9cf"))+
scale_fill_gradientn(colours=c("white","#d1e5f0","#92c5de","#4393c3","#2166ac"), na.value = "grey98",limits = c(0, 100))+
#scale_fill_gradientn(colours=c("#fddbc7","#f4a582","#d6604d","#b2182b"), na.value = "grey98",limits = c(10, 40))+
#scale_color_gradientn(colours=c("#b2182b","#fddbc7","white","#d1e5f0","#67a9cf", "#67a9cf", "#2166ac"), na.value = "grey98",limits = c(-0, 40))+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5, hjust=0.95, size=12),
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),
panel.background= element_rect(fill=NA, color='black'),
legend.title = element_blank(),
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_blank(),
strip.text = element_text(size=12))#making the axis title larger
freq_fig_down
compare_figs_all<-cowplot::plot_grid(freq_fig_up, freq_fig_down, ncol=2, align="h")
compare_figs_all
biomin_mod <-read.csv("../../../output/WGCNA/Biomineralization_toolkit_by_module.csv")
head(biomin_mod)## X Pocillopora_acuta_best_hit accessionnumber.geneID
## 1 225 Pocillopora_acuta_HIv2___RNAseq.g10093.t2 XP_022804785.1
## 2 608 Pocillopora_acuta_HIv2___RNAseq.g11609.t1 P33_g8985
## 3 1253 Pocillopora_acuta_HIv2___RNAseq.g13824.t1 Gene:g27814
## 4 1427 Pocillopora_acuta_HIv2___RNAseq.g14505.t1 Gene:g9094
## 5 1466 Pocillopora_acuta_HIv2___RNAseq.g14663.t1a PFX27832.1
## 6 1642 Pocillopora_acuta_HIv2___RNAseq.g15280.t1 AJQ31790.1
## definition
## 1 thioredoxin reductase 1, cytoplasmic-like [Stylophora pistillata]
## 2 Flagellar associated protein
## 3 Annotated: carbonic anhydrase (STPCA2-2)
## 4 Annotated: Actin
## 5 Poly [ADP-ribose] polymerase 11 [Stylophora pistillata]
## 6 solute carrier family 4 member gamma [Stylophora pistillata]
## Ref substanceBXH
## 1 Peled et al., 2020 Pocillopora_acuta_HIv2___RNAseq.g10093.t2
## 2 Drake et al., 2013 Pocillopora_acuta_HIv2___RNAseq.g11609.t1
## 3 Mummadisetti et al., 2021 Pocillopora_acuta_HIv2___RNAseq.g13824.t1
## 4 Mummadisetti et al., 2021 Pocillopora_acuta_HIv2___RNAseq.g14505.t1
## 5 Peled et al., 2020 Pocillopora_acuta_HIv2___RNAseq.g14663.t1a
## 6 Zoccola et al., 2015 Pocillopora_acuta_HIv2___RNAseq.g15280.t1
## geneSymbol moduleColor
## 1 Pocillopora_acuta_HIv2___Sc0000021 blue
## 2 Pocillopora_acuta_HIv2___Sc0000013 turquoise
## 3 Pocillopora_acuta_HIv2___Sc0000005 blue
## 4 Pocillopora_acuta_HIv2___xfSc0000036 turquoise
## 5 Pocillopora_acuta_HIv2___Sc0000020 turquoise
## 6 Pocillopora_acuta_HIv2___Sc0000006 pink
## GO.terms
## 1 GO:0000003,GO:0000302,GO:0000305,GO:0001650,GO:0001704,GO:0001707,GO:0001887,GO:0001890,GO:0003006,GO:0003674,GO:0003824,GO:0004791,GO:0005488,GO:0005515,GO:0005575,GO:0005622,GO:0005623,GO:0005634,GO:0005654,GO:0005730,GO:0005737,GO:0005739,GO:0005783,GO:0005829,GO:0006082,GO:0006139,GO:0006518,GO:0006520,GO:0006575,GO:0006725,GO:0006732,GO:0006733,GO:0006739,GO:0006749,GO:0006753,GO:0006790,GO:0006793,GO:0006796,GO:0006807,GO:0006950,GO:0006979,GO:0007154,GO:0007165,GO:0007275,GO:0007369,GO:0007498,GO:0008150,GO:0008152,GO:0008283,GO:0009056,GO:0009069,GO:0009117,GO:0009611,GO:0009628,GO:0009636,GO:0009653,GO:0009790,GO:0009888,GO:0009987,GO:0010035,GO:0010038,GO:0010269,GO:0010941,GO:0010942,GO:0012505,GO:0015036,GO:0015949,GO:0016043,GO:0016174,GO:0016209,GO:0016259,GO:0016491,GO:0016651,GO:0016667,GO:0016668,GO:0016999,GO:0017001,GO:0017144,GO:0018996,GO:0019216,GO:0019222,GO:0019362,GO:0019637,GO:0019725,GO:0019752,GO:0022404,GO:0022414,GO:0022607,GO:0023052,GO:0031974,GO:0031981,GO:0032501,GO:0032502,GO:0033554,GO:0033797,GO:0034599,GO:0034641,GO:0036295,GO:0036296,GO:0036477,GO:0042221,GO:0042303,GO:0042395,GO:0042493,GO:0042537,GO:0042592,GO:0042737,GO:0042743,GO:0042744,GO:0042802,GO:0042803,GO:0043025,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043228,GO:0043229,GO:0043231,GO:0043232,GO:0043233,GO:0043436,GO:0043603,GO:0043933,GO:0044085,GO:0044237,GO:0044238,GO:0044248,GO:0044281,GO:0044297,GO:0044422,GO:0044424,GO:0044428,GO:0044444,GO:0044446,GO:0044452,GO:0044464,GO:0045340,GO:0045454,GO:0046483,GO:0046496,GO:0046688,GO:0046872,GO:0046914,GO:0046983,GO:0048332,GO:0048513,GO:0048518,GO:0048522,GO:0048598,GO:0048608,GO:0048646,GO:0048678,GO:0048729,GO:0048731,GO:0048856,GO:0050664,GO:0050789,GO:0050794,GO:0050896,GO:0051186,GO:0051187,GO:0051259,GO:0051262,GO:0051716,GO:0055086,GO:0055093,GO:0055114,GO:0061458,GO:0065003,GO:0065007,GO:0065008,GO:0070013,GO:0070276,GO:0070482,GO:0070887,GO:0070995,GO:0071241,GO:0071248,GO:0071280,GO:0071453,GO:0071455,GO:0071704,GO:0071840,GO:0072524,GO:0072593,GO:0080090,GO:0097237,GO:0097458,GO:0098623,GO:0098625,GO:0098626,GO:0098754,GO:0098869,GO:1901360,GO:1901564,GO:1901605,GO:1901700,GO:1990748
## 2 -
## 3 GO:0003674,GO:0003824,GO:0004064,GO:0004089,GO:0005575,GO:0005622,GO:0005623,GO:0005737,GO:0005829,GO:0006810,GO:0006811,GO:0006820,GO:0007154,GO:0007165,GO:0007166,GO:0008150,GO:0009987,GO:0010033,GO:0015701,GO:0015711,GO:0016787,GO:0016788,GO:0016829,GO:0016835,GO:0016836,GO:0019221,GO:0023052,GO:0034097,GO:0035722,GO:0042221,GO:0044424,GO:0044444,GO:0044464,GO:0050789,GO:0050794,GO:0050896,GO:0051179,GO:0051234,GO:0051716,GO:0052689,GO:0065007,GO:0070671,GO:0070887,GO:0071310,GO:0071345,GO:0071349,GO:0071702
## 4 GO:0000123,GO:0000278,GO:0000281,GO:0000910,GO:0003674,GO:0005198,GO:0005200,GO:0005575,GO:0005622,GO:0005623,GO:0005634,GO:0005654,GO:0005737,GO:0005856,GO:0005884,GO:0005886,GO:0005912,GO:0005924,GO:0005925,GO:0006325,GO:0006338,GO:0006464,GO:0006473,GO:0006475,GO:0006807,GO:0006996,GO:0007010,GO:0007015,GO:0007049,GO:0007275,GO:0007507,GO:0007517,GO:0007519,GO:0007528,GO:0008150,GO:0008152,GO:0009653,GO:0009888,GO:0009987,GO:0010927,GO:0014706,GO:0014866,GO:0014902,GO:0014904,GO:0015629,GO:0016020,GO:0016043,GO:0016569,GO:0016570,GO:0016573,GO:0018193,GO:0018205,GO:0018393,GO:0018394,GO:0019538,GO:0022402,GO:0022607,GO:0030029,GO:0030036,GO:0030054,GO:0030055,GO:0030154,GO:0030239,GO:0031032,GO:0031248,GO:0031974,GO:0031981,GO:0032501,GO:0032502,GO:0032989,GO:0032991,GO:0034728,GO:0035267,GO:0036211,GO:0042692,GO:0043044,GO:0043170,GO:0043189,GO:0043226,GO:0043227,GO:0043228,GO:0043229,GO:0043231,GO:0043232,GO:0043233,GO:0043412,GO:0043486,GO:0043543,GO:0043933,GO:0044085,GO:0044237,GO:0044238,GO:0044260,GO:0044267,GO:0044422,GO:0044424,GO:0044428,GO:0044430,GO:0044444,GO:0044446,GO:0044451,GO:0044464,GO:0048468,GO:0048513,GO:0048646,GO:0048731,GO:0048741,GO:0048747,GO:0048856,GO:0048869,GO:0050789,GO:0050794,GO:0050803,GO:0050807,GO:0050808,GO:0051128,GO:0051146,GO:0051276,GO:0051301,GO:0055001,GO:0055002,GO:0060537,GO:0060538,GO:0061061,GO:0061640,GO:0065007,GO:0065008,GO:0070013,GO:0070161,GO:0070925,GO:0071689,GO:0071704,GO:0071824,GO:0071840,GO:0071944,GO:0072359,GO:0097433,GO:0097435,GO:0098529,GO:0099080,GO:0099081,GO:0099512,GO:0099513,GO:1901564,GO:1902493,GO:1902494,GO:1902562,GO:1903047,GO:1990234
## 5 GO:0000003,GO:0001067,GO:0001501,GO:0001568,GO:0001570,GO:0001655,GO:0001822,GO:0001944,GO:0002376,GO:0002520,GO:0003006,GO:0003674,GO:0003676,GO:0003677,GO:0003824,GO:0003950,GO:0005488,GO:0005575,GO:0005622,GO:0005623,GO:0005634,GO:0006464,GO:0006471,GO:0006629,GO:0006807,GO:0007154,GO:0007165,GO:0007166,GO:0007167,GO:0007169,GO:0007275,GO:0007548,GO:0008150,GO:0008152,GO:0008202,GO:0008209,GO:0008210,GO:0008406,GO:0008585,GO:0009653,GO:0009791,GO:0009887,GO:0009888,GO:0009892,GO:0009893,GO:0009894,GO:0009896,GO:0009987,GO:0010033,GO:0010171,GO:0010468,GO:0010604,GO:0010605,GO:0010629,GO:0010817,GO:0014070,GO:0016740,GO:0016757,GO:0016763,GO:0019222,GO:0019538,GO:0022414,GO:0023052,GO:0030097,GO:0030154,GO:0032501,GO:0032502,GO:0034754,GO:0035239,GO:0035295,GO:0035326,GO:0036211,GO:0042176,GO:0042221,GO:0042445,GO:0043170,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0043412,GO:0044212,GO:0044237,GO:0044238,GO:0044260,GO:0044267,GO:0044424,GO:0044464,GO:0045137,GO:0045732,GO:0046545,GO:0046660,GO:0048008,GO:0048513,GO:0048514,GO:0048518,GO:0048519,GO:0048534,GO:0048608,GO:0048705,GO:0048731,GO:0048745,GO:0048856,GO:0048869,GO:0050789,GO:0050794,GO:0050896,GO:0051171,GO:0051173,GO:0051246,GO:0051247,GO:0051716,GO:0060021,GO:0060255,GO:0060322,GO:0060323,GO:0060324,GO:0060325,GO:0060537,GO:0061458,GO:0065007,GO:0065008,GO:0070887,GO:0071310,GO:0071407,GO:0071704,GO:0072001,GO:0072358,GO:0072359,GO:0080090,GO:0097159,GO:1901360,GO:1901363,GO:1901564
## 6 GO:0000003,GO:0003674,GO:0005215,GO:0005452,GO:0005488,GO:0005515,GO:0005575,GO:0005623,GO:0005886,GO:0005887,GO:0006810,GO:0006811,GO:0006812,GO:0006814,GO:0006820,GO:0006821,GO:0006873,GO:0006885,GO:0007275,GO:0007276,GO:0007283,GO:0008150,GO:0008324,GO:0008509,GO:0008510,GO:0008514,GO:0009987,GO:0015075,GO:0015077,GO:0015081,GO:0015103,GO:0015106,GO:0015108,GO:0015291,GO:0015293,GO:0015294,GO:0015297,GO:0015301,GO:0015318,GO:0015370,GO:0015672,GO:0015698,GO:0015701,GO:0015711,GO:0016020,GO:0016021,GO:0016323,GO:0016324,GO:0019725,GO:0019899,GO:0019953,GO:0022414,GO:0022804,GO:0022857,GO:0022890,GO:0030001,GO:0030003,GO:0030004,GO:0030641,GO:0031224,GO:0031226,GO:0032501,GO:0032502,GO:0032504,GO:0034220,GO:0035295,GO:0035725,GO:0042592,GO:0044425,GO:0044459,GO:0044464,GO:0044703,GO:0045177,GO:0046873,GO:0048232,GO:0048565,GO:0048609,GO:0048731,GO:0048856,GO:0048878,GO:0050801,GO:0051179,GO:0051234,GO:0051453,GO:0051704,GO:0055067,GO:0055080,GO:0055082,GO:0055085,GO:0055123,GO:0065007,GO:0065008,GO:0071702,GO:0071944,GO:0098590,GO:0098655,GO:0098656,GO:0098660,GO:0098661,GO:0098662,GO:0098771,GO:0099516,GO:1902476
## GO.description GS.Flat GS.Slope
## 1 thioredoxin-disulfide reductase activity 0.57190344 -0.57190344
## 2 - -0.29615673 0.29615673
## 3 carbonate dehydratase activity 0.82284313 -0.82284313
## 4 belongs to the actin family -0.44984287 0.44984287
## 5 TCDD-inducible poly ADP-ribose polymerase 0.04277864 -0.04277864
## 6 sodium:bicarbonate symporter activity 0.42124084 -0.42124084
## p.GS.Flat p.GS.Slope A.blue p.A.blue A.black p.A.black
## 1 3.296265e-05 3.296265e-05 0.6816236 1.839243e-07 -0.5833475 2.093028e-05
## 2 4.566951e-02 4.566951e-02 -0.4736549 8.846259e-04 0.4149787 4.135812e-03
## 3 2.282405e-12 2.282405e-12 0.9065745 4.306626e-18 -0.8069304 1.271757e-11
## 4 1.709469e-03 1.709469e-03 -0.5188606 2.204480e-04 0.5872458 1.785967e-05
## 5 7.777263e-01 7.777263e-01 -0.1544002 3.055833e-01 0.2095712 1.621606e-01
## 6 3.552683e-03 3.552683e-03 0.5190538 2.190498e-04 -0.6416509 1.544375e-06
## A.pink p.A.pink A.red p.A.red A.salmon p.A.salmon
## 1 0.27842751 6.097779e-02 -0.4083356 4.844425e-03 -0.7472873 2.437181e-09
## 2 -0.34099292 2.039159e-02 0.2228543 1.365748e-01 0.1622026 2.814859e-01
## 3 0.63501061 2.135745e-06 -0.6408045 1.610223e-06 -0.7482656 2.262822e-09
## 4 -0.39257347 6.963855e-03 0.1921334 2.008242e-01 0.3122323 3.464228e-02
## 5 -0.06841708 6.514225e-01 0.1073470 4.776535e-01 0.2320335 1.207387e-01
## 6 0.75371159 1.487555e-09 -0.6357069 2.065103e-06 -0.4624218 1.214176e-03
## A.greenyellow p.A.greenyellow A.turquoise p.A.turquoise A.cyan
## 1 0.6739431 2.838963e-07 -0.3330385 2.372177e-02 0.4267480
## 2 -0.1594412 2.898678e-01 0.5857920 1.895275e-05 -0.1271445
## 3 0.6280105 2.981403e-06 -0.4792416 7.526735e-04 0.5051039
## 4 -0.2841205 5.566998e-02 0.7612393 8.180878e-10 -0.4620600
## 5 -0.1447235 3.372496e-01 0.2102914 1.606897e-01 -0.1723410
## 6 0.0948033 5.308520e-01 -0.1847180 2.190911e-01 0.2164040
## p.A.cyan A.brown p.A.brown A.lightcyan p.A.lightcyan A.tan
## 1 0.0031008521 0.1271912 3.995972e-01 0.09110039 0.54709232 0.2176203
## 2 0.3997716440 -0.5933724 1.386015e-05 0.18659720 0.21435658 0.1819197
## 3 0.0003434504 0.3135143 3.386687e-02 0.22821859 0.12714273 0.1574452
## 4 0.0012264089 -0.7407478 3.969181e-09 0.33357821 0.02348224 0.0636769
## 5 0.2520848072 -0.3626069 1.326528e-02 0.18378842 0.22145957 0.4510512
## 6 0.1485953064 0.2471506 9.773671e-02 0.32845822 0.02583794 -0.2762368
## p.A.tan A.green p.A.green A.purple p.A.purple A.magenta
## 1 0.146270907 0.09661801 0.5229802445 0.08334567 5.818526e-01 -0.33576335
## 2 0.226274419 -0.21911333 0.1434547172 -0.15787549 2.946916e-01 -0.19726405
## 3 0.296026422 0.10379593 0.4924217545 0.29166711 4.921348e-02 -0.08868698
## 4 0.674179118 -0.50372335 0.0003587078 -0.06971277 6.452552e-01 -0.13140604
## 5 0.001655126 0.09486416 0.5305870974 -0.22683689 1.295240e-01 0.16146684
## 6 0.063125044 -0.23054378 0.1232098351 0.80793923 1.145965e-11 0.12353209
## p.A.magenta A.midnightblue p.A.midnightblue A.grey60 p.A.grey60
## 1 0.02253312 0.009700231 0.94898532 -0.0273657 0.856737263
## 2 0.18883104 0.100592699 0.50594353 -0.1887542 0.209010743
## 3 0.55780330 0.045801753 0.76245981 0.1449134 0.336609140
## 4 0.38402987 -0.094778219 0.53096122 -0.3901718 0.007348835
## 5 0.28370346 0.338323606 0.02146223 -0.2737761 0.065608424
## 6 0.41340438 -0.124918253 0.40814208 0.2161768 0.149032326glmmseq_exp <-read.csv("../../../output/Slope_Base/model_expression_prediction_allgenes.csv")
glmmseq_exp <- plyr::rename(glmmseq_exp, c("X"="Pocillopora_acuta_best_hit"))biomin_exp <- merge(biomin_mod, glmmseq_exp, by=c("Pocillopora_acuta_best_hit"), all.x=T)write.csv(biomin_exp, "../../../output/WGCNA/Biomineralization_toolkit_glmmseq_expression.csv")biomin_all <-read.csv("../../../output/Biomin_blast_Pocillopora_acuta_best_hit_glmmSeq.csv")
head(biomin_all)## Gene Dispersion AIC logLik
## 1 Pocillopora_acuta_HIv2___RNAseq.g13823.t1 0.29270610 366.4332 -177.2166
## 2 Pocillopora_acuta_HIv2___RNAseq.g13823.t1 0.29270610 366.4332 -177.2166
## 3 Pocillopora_acuta_HIv2___RNAseq.g13823.t1 0.29270610 366.4332 -177.2166
## 4 Pocillopora_acuta_HIv2___RNAseq.g25351.t1 0.13435721 815.9720 -401.9860
## 5 Pocillopora_acuta_HIv2___RNAseq.g7085.t1 0.25162583 491.9378 -239.9689
## 6 Pocillopora_acuta_HIv2___RNAseq.g22851.t1 0.02235176 759.7088 -373.8544
## meanExp X.Intercept. TreatmentVariable OriginFlat
## 1 4.316132 3.079614 0.16922532 0.07545055
## 2 4.316132 3.079614 0.16922532 0.07545055
## 3 4.316132 3.079614 0.16922532 0.07545055
## 4 12.237463 8.288576 -0.01709198 0.40440178
## 5 6.477549 4.543751 -0.19119978 0.09230384
## 6 11.722317 8.185091 -0.11783143 -0.07240262
## TreatmentVariable.OriginFlat se_.Intercept. se_TreatmentVariable
## 1 -0.3792527 0.1679989 0.2363277
## 2 -0.3792527 0.1679989 0.2363277
## 3 -0.3792527 0.1679989 0.2363277
## 4 0.2217089 0.1059042 0.1497752
## 5 0.3564220 0.1641296 0.2123867
## 6 0.1972383 0.0571238 0.0618745
## se_OriginFlat se_TreatmentVariable.OriginFlat Chisq_Treatment Chisq_Origin
## 1 0.24229985 0.34311487 0.003896091 0.4390691
## 2 0.24229985 0.34311487 0.003896091 0.4390691
## 3 0.24229985 0.34311487 0.003896091 0.4390691
## 4 0.15311285 0.21653465 0.676680451 22.6483669
## 5 0.22652466 0.30543197 0.013908932 2.6586173
## 6 0.08256803 0.08945199 0.275523829 0.1398413
## Chisq_Treatment.Origin Df_Treatment Df_Origin Df_Treatment.Origin P_Treatment
## 1 1.221739 1 1 1 0.9502294
## 2 1.221739 1 1 1 0.9502294
## 3 1.221739 1 1 1 0.9502294
## 4 1.048362 1 1 1 0.4107321
## 5 1.361758 1 1 1 0.9061183
## 6 4.861862 1 1 1 0.5996502
## P_Origin P_Treatment.Origin Treatment Origin Treatment.Origin
## 1 5.075721e-01 0.26901967 1 0.5306740470 0.9994279
## 2 5.075721e-01 0.26901967 1 0.5306740470 0.9994279
## 3 5.075721e-01 0.26901967 1 0.5306740470 0.9994279
## 4 1.945255e-06 0.30588455 1 0.0001683701 0.9994279
## 5 1.029902e-01 0.24323297 1 0.2466098058 0.9994279
## 6 7.084388e-01 0.02745669 1 0.6038776397 0.9994279
## Stable_OriginFC Variable_OriginFC maxGroupFC col RF13B
## 1 -0.1042361 0.4192811 Variable Not Significant 21.57376
## 2 -0.1042361 0.4192811 Variable Not Significant 21.57376
## 3 -0.1042361 0.4192811 Variable Not Significant 21.57376
## 4 -0.5833078 -0.9031151 Variable q_Origin < 0.05 5832.10758
## 5 -0.1318273 -0.6407294 Variable Not Significant 67.80326
## 6 0.1044247 -0.1800468 Variable Not Significant 4739.03686
## RF13D RF14B RF14C RF15B RF15D RF17B RF17D
## 1 25.50848 16.94826 19.20733 28.23482 21.29134 25.87585 14.01704
## 2 25.50848 16.94826 19.20733 28.23482 21.29134 25.87585 14.01704
## 3 25.50848 16.94826 19.20733 28.23482 21.29134 25.87585 14.01704
## 4 4927.06132 13021.91653 6113.26692 5054.03248 7484.79414 8321.89749 7240.96832
## 5 70.63887 54.61107 99.23788 164.36698 112.66669 121.50398 91.11075
## 6 4597.41325 2757.85926 3654.72843 3468.84911 3098.77752 2764.21551 2954.09080
## RF18B RF18D RF19B RF19C RF20B RF20C RF22B
## 1 22.30905 43.47845 0.0000 24.20314 34.69447 16.42775 13.92415
## 2 22.30905 43.47845 0.0000 24.20314 34.69447 16.42775 13.92415
## 3 22.30905 43.47845 0.0000 24.20314 34.69447 16.42775 13.92415
## 4 5891.93841 5089.20850 8016.9416 8866.41520 4982.12595 8081.53904 7060.31604
## 5 123.28687 101.44972 118.3772 140.60869 115.64823 135.98524 42.54600
## 6 2417.59689 3150.51549 3524.0588 2869.80032 3728.49908 2716.05423 4221.33720
## RF22C RF23A RF23C RF24B RF24D RF25A RF25C
## 1 18.19144 18.60133 36.2419 18.57332 23.35614 10.69681 16.36654
## 2 18.19144 18.60133 36.2419 18.57332 23.35614 10.69681 16.36654
## 3 18.19144 18.60133 36.2419 18.57332 23.35614 10.69681 16.36654
## 4 3512.96929 6530.04515 4346.0891 4820.26566 5124.51037 6260.69212 4758.11817
## 5 46.48924 249.64940 184.1480 184.75567 70.06842 92.45103 98.19927
## 6 3153.18302 3553.83267 3132.4753 3154.53200 3760.33872 3892.11199 3634.28212
## RS11B RS11D RS12A RS12C RS13A RS13C RS14B
## 1 37.03275 14.09808 0.00000 8.755265 20.55198 15.25056 29.16535
## 2 37.03275 14.09808 0.00000 8.755265 20.55198 15.25056 29.16535
## 3 37.03275 14.09808 0.00000 8.755265 20.55198 15.25056 29.16535
## 4 4408.84668 3804.31239 2168.53312 3681.588844 2701.11675 2417.21364 3177.56482
## 5 75.04005 300.39753 20.40972 12.257371 104.71721 80.06544 85.30865
## 6 3502.51878 3288.10581 3286.98596 2969.785817 3332.35599 3746.87177 3115.58845
## RS14C RS15B RS15D RS1B RS1C RS2B RS2C
## 1 14.95038 17.20235 15.77586 6.823476 33.59846 34.30448 35.76535
## 2 14.95038 17.20235 15.77586 6.823476 33.59846 34.30448 35.76535
## 3 14.95038 17.20235 15.77586 6.823476 33.59846 34.30448 35.76535
## 4 3123.75088 2933.85998 3892.69273 3421.973109 3717.90918 6782.61209 5170.97795
## 5 73.87249 85.15161 46.01292 55.725052 95.99559 59.81295 85.37536
## 6 3313.70871 3593.56992 3662.62815 3472.011931 3480.80008 2515.66212 3603.07098
## RS3B RS3D RS6A RS6D RS7B RS7C RS8B
## 1 44.72649 29.74233 29.32862 38.32429 30.78679 17.29086 9.894721
## 2 44.72649 29.74233 29.32862 38.32429 30.78679 17.29086 9.894721
## 3 44.72649 29.74233 29.32862 38.32429 30.78679 17.29086 9.894721
## 4 5164.93773 4277.13888 5058.41471 4024.05055 2932.44205 5029.82092 3791.477100
## 5 118.62244 77.71383 61.74446 120.29569 71.46934 82.81413 52.172164
## 6 2804.15671 2625.00044 3068.69956 3619.51637 3201.82649 3680.22360 3224.779455
## RS8C RS9A RS9C accessionnumber.geneID
## 1 14.95208 47.19477 19.44197 aug_v2a.09809.t1
## 2 14.95208 47.19477 19.44197 P13_g6918
## 3 14.95208 47.19477 19.44197 PFX18785.1
## 4 4200.60065 4097.88734 3391.45658 XP_022794351.1
## 5 75.69492 145.03759 102.65358 XP_022799541.1
## 6 3453.93103 2906.50718 4526.08973 P4_g9861
## definition
## 1 Mucin4-like protein
## 2 Sushi domain-containing
## 3 Mucin-4 [Stylophora pistillata]
## 4 mammalian ependymin-related protein 1-like [Stylophora pistillata]
## 5 uncharacterized protein LOC111337489 [Stylophora pistillata]
## 6 Viral inclusion protein
## Ref
## 1 Takeuchi et al., 2016
## 2 Drake et al., 2013
## 3 Peled et al., 2020
## 4 Peled et al., 2020
## 5 Peled et al., 2020
## 6 Drake et al., 2013library(tidyr)
biomin_all_filtered_long <- pivot_longer(biomin_all, cols=30:75, names_to = "Colony", values_to = "Expression")
biomin_all_filtered_long$Colony <- as.factor(biomin_all_filtered_long$Colony)
head(biomin_all_filtered_long)## # A tibble: 6 × 34
## Gene Dispersion AIC logLik meanExp X.Intercept. TreatmentVariable
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Pocillopora_ac… 0.293 366. -177. 4.32 3.08 0.169
## 2 Pocillopora_ac… 0.293 366. -177. 4.32 3.08 0.169
## 3 Pocillopora_ac… 0.293 366. -177. 4.32 3.08 0.169
## 4 Pocillopora_ac… 0.293 366. -177. 4.32 3.08 0.169
## 5 Pocillopora_ac… 0.293 366. -177. 4.32 3.08 0.169
## 6 Pocillopora_ac… 0.293 366. -177. 4.32 3.08 0.169
## # ℹ 27 more variables: OriginFlat <dbl>, TreatmentVariable.OriginFlat <dbl>,
## # se_.Intercept. <dbl>, se_TreatmentVariable <dbl>, se_OriginFlat <dbl>,
## # se_TreatmentVariable.OriginFlat <dbl>, Chisq_Treatment <dbl>,
## # Chisq_Origin <dbl>, Chisq_Treatment.Origin <dbl>, Df_Treatment <int>,
## # Df_Origin <int>, Df_Treatment.Origin <int>, P_Treatment <dbl>,
## # P_Origin <dbl>, P_Treatment.Origin <dbl>, Treatment <dbl>, Origin <dbl>,
## # Treatment.Origin <dbl>, Stable_OriginFC <dbl>, Variable_OriginFC <dbl>, …biomin_all_filtered_long <- biomin_all_filtered_long %>%
separate(Colony, into = c('Origin', 'Colony.number'), sep = 2)
library(stringr)
biomin_all_filtered_long$Colony <- as.numeric(str_extract(biomin_all_filtered_long$Colony.number, "[0-9]+"))
biomin_all_filtered_long <- biomin_all_filtered_long %>%
mutate(Treatment = trimws(str_remove(biomin_all_filtered_long$Colony.number, "(\\s+[A-Za-z]+)?[0-9-]+")))
biomin_all_filtered_long$Origin <- as.factor(biomin_all_filtered_long$Origin)
biomin_all_filtered_long$Treatment <- as.factor(biomin_all_filtered_long$Treatment)
biomin_all_filtered_long <- biomin_all_filtered_long %>%
mutate(Treatment2 = ifelse(Treatment == "A" | Treatment == "B", "Variable",
ifelse(Treatment == "C" | Treatment == "D", "Stable", NA)))
biomin_all_filtered_long$Treatment2 <- as.factor(biomin_all_filtered_long$Treatment2)
head(biomin_all_filtered_long)## # A tibble: 6 × 36
## Gene Dispersion AIC logLik meanExp X.Intercept. TreatmentVariable
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Pocillopora_ac… 0.293 366. -177. 4.32 3.08 0.169
## 2 Pocillopora_ac… 0.293 366. -177. 4.32 3.08 0.169
## 3 Pocillopora_ac… 0.293 366. -177. 4.32 3.08 0.169
## 4 Pocillopora_ac… 0.293 366. -177. 4.32 3.08 0.169
## 5 Pocillopora_ac… 0.293 366. -177. 4.32 3.08 0.169
## 6 Pocillopora_ac… 0.293 366. -177. 4.32 3.08 0.169
## # ℹ 29 more variables: OriginFlat <dbl>, TreatmentVariable.OriginFlat <dbl>,
## # se_.Intercept. <dbl>, se_TreatmentVariable <dbl>, se_OriginFlat <dbl>,
## # se_TreatmentVariable.OriginFlat <dbl>, Chisq_Treatment <dbl>,
## # Chisq_Origin <dbl>, Chisq_Treatment.Origin <dbl>, Df_Treatment <int>,
## # Df_Origin <int>, Df_Treatment.Origin <int>, P_Treatment <dbl>,
## # P_Origin <dbl>, P_Treatment.Origin <dbl>, Treatment <fct>,
## # Treatment.Origin <dbl>, Stable_OriginFC <dbl>, Variable_OriginFC <dbl>, …#MEBlue signficant genes ##Thioredoxin reductase 1
biomin_all_filtered_long_g10093 <- biomin_all_filtered_long %>% filter(Gene == "Pocillopora_acuta_HIv2___RNAseq.g10093.t2")
biomin_all_filtered_long_g10093 ## # A tibble: 46 × 36
## Gene Dispersion AIC logLik meanExp X.Intercept. TreatmentVariable
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Pocillopora_a… 0.0876 385. -187. 5.74 3.88 -0.142
## 2 Pocillopora_a… 0.0876 385. -187. 5.74 3.88 -0.142
## 3 Pocillopora_a… 0.0876 385. -187. 5.74 3.88 -0.142
## 4 Pocillopora_a… 0.0876 385. -187. 5.74 3.88 -0.142
## 5 Pocillopora_a… 0.0876 385. -187. 5.74 3.88 -0.142
## 6 Pocillopora_a… 0.0876 385. -187. 5.74 3.88 -0.142
## 7 Pocillopora_a… 0.0876 385. -187. 5.74 3.88 -0.142
## 8 Pocillopora_a… 0.0876 385. -187. 5.74 3.88 -0.142
## 9 Pocillopora_a… 0.0876 385. -187. 5.74 3.88 -0.142
## 10 Pocillopora_a… 0.0876 385. -187. 5.74 3.88 -0.142
## # ℹ 36 more rows
## # ℹ 29 more variables: OriginFlat <dbl>, TreatmentVariable.OriginFlat <dbl>,
## # se_.Intercept. <dbl>, se_TreatmentVariable <dbl>, se_OriginFlat <dbl>,
## # se_TreatmentVariable.OriginFlat <dbl>, Chisq_Treatment <dbl>,
## # Chisq_Origin <dbl>, Chisq_Treatment.Origin <dbl>, Df_Treatment <int>,
## # Df_Origin <int>, Df_Treatment.Origin <int>, P_Treatment <dbl>,
## # P_Origin <dbl>, P_Treatment.Origin <dbl>, Treatment <fct>, …library(nlme)##
## Attaching package: 'nlme'## The following object is masked from 'package:IRanges':
##
## collapse## The following object is masked from 'package:dplyr':
##
## collapselibrary(emmeans)## Warning: package 'emmeans' was built under R version 4.3.1g10093.lme <- lme(Expression~Origin*Treatment2, random = ~1|Colony, data=biomin_all_filtered_long_g10093 , na.action=na.exclude)
car::Anova(g10093.lme, type=3)## Analysis of Deviance Table (Type III tests)
##
## Response: Expression
## Chisq Df Pr(>Chisq)
## (Intercept) 205.6032 1 < 2.2e-16 ***
## Origin 10.8768 1 0.0009738 ***
## Treatment2 0.2141 1 0.6435866
## Origin:Treatment2 1.3642 1 0.2428065
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1tukey3 <- emmeans(g10093.lme, list(pairwise ~ Origin), adjust = "tukey")## NOTE: Results may be misleading due to involvement in interactionstukey3## $`emmeans of Origin`
## Origin emmean SE df lower.CL upper.CL
## RF 66.4 3.89 19 58.2 74.5
## RS 43.9 3.76 19 36.0 51.7
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containment
## Confidence level used: 0.95
##
## $`pairwise differences of Origin`
## 1 estimate SE df t.ratio p.value
## RF - RS 22.5 4.63 23 4.862 0.0001
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containmentlibrary(Rmisc)
g10093_sum<-summarySE(biomin_all_filtered_long_g10093 , measurevar='Expression', groupvars=c('Origin', 'Treatment2'), na.rm=TRUE, conf.interval = 0.95)
g10093_sum## Origin Treatment2 N Expression sd se ci
## 1 RF Stable 11 63.79961 16.37758 4.938025 11.002606
## 2 RF Variable 11 65.98269 22.07239 6.655076 14.828433
## 3 RS Stable 12 47.40346 10.98308 3.170542 6.978315
## 4 RS Variable 12 41.95704 10.53729 3.041854 6.695076###Figure
pd<- position_dodge(0.2)
g10093_fig<-ggplot(data=g10093_sum, aes(y=Expression, x=Treatment2, color=Origin),group = interaction(Origin))+
geom_point(data=biomin_all_filtered_long_g10093,aes(y=Expression, x=Treatment2, color=Origin), alpha=0.4, position = pd)+
geom_line(aes(group = interaction(Origin), stat="identity"),position=position_dodge(0.2))+
geom_point(size=3, stat="identity", position = pd)+
geom_errorbar(aes(ymin=Expression-se, ymax=Expression+se), stat="identity",width=0.2, position = pd)+
scale_fill_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_color_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_y_continuous(expression(Thioredoxin~reductase~1))+
ggtitle(~blue)+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5,size=12),#angling the labels on the x-axis
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),#telling it where to position our plot title
panel.background= element_rect(fill=NA, color='black'),#this is making the black box around the graph
#strip.background = element_blank(),
#strip.text = element_blank(),
legend.title = element_text(vjust=0.5,size=12),
legend.position="none",
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_text(size=12))#making the axis title larger ## Warning in geom_line(aes(group = interaction(Origin), stat = "identity"), :
## Ignoring unknown aesthetics: statg10093_fig
##Carbonic anhydrase - STPCA2-2
biomin_all_filtered_long_g13824 <- biomin_all_filtered_long %>%
filter(Gene == "Pocillopora_acuta_HIv2___RNAseq.g13824.t1")
biomin_all_filtered_long_g13824 ## # A tibble: 46 × 36
## Gene Dispersion AIC logLik meanExp X.Intercept. TreatmentVariable
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Pocillopora_a… 2.35 453. -220. 4.66 2.36 -0.0648
## 2 Pocillopora_a… 2.35 453. -220. 4.66 2.36 -0.0648
## 3 Pocillopora_a… 2.35 453. -220. 4.66 2.36 -0.0648
## 4 Pocillopora_a… 2.35 453. -220. 4.66 2.36 -0.0648
## 5 Pocillopora_a… 2.35 453. -220. 4.66 2.36 -0.0648
## 6 Pocillopora_a… 2.35 453. -220. 4.66 2.36 -0.0648
## 7 Pocillopora_a… 2.35 453. -220. 4.66 2.36 -0.0648
## 8 Pocillopora_a… 2.35 453. -220. 4.66 2.36 -0.0648
## 9 Pocillopora_a… 2.35 453. -220. 4.66 2.36 -0.0648
## 10 Pocillopora_a… 2.35 453. -220. 4.66 2.36 -0.0648
## # ℹ 36 more rows
## # ℹ 29 more variables: OriginFlat <dbl>, TreatmentVariable.OriginFlat <dbl>,
## # se_.Intercept. <dbl>, se_TreatmentVariable <dbl>, se_OriginFlat <dbl>,
## # se_TreatmentVariable.OriginFlat <dbl>, Chisq_Treatment <dbl>,
## # Chisq_Origin <dbl>, Chisq_Treatment.Origin <dbl>, Df_Treatment <int>,
## # Df_Origin <int>, Df_Treatment.Origin <int>, P_Treatment <dbl>,
## # P_Origin <dbl>, P_Treatment.Origin <dbl>, Treatment <fct>, …library(nlme)
g13824.lme <- lme(Expression~Origin*Treatment2, random = ~1|Colony, data=biomin_all_filtered_long_g13824 , na.action=na.exclude)
car::Anova(g13824.lme, type=3)## Analysis of Deviance Table (Type III tests)
##
## Response: Expression
## Chisq Df Pr(>Chisq)
## (Intercept) 77.9228 1 <2e-16 ***
## Origin 78.0753 1 <2e-16 ***
## Treatment2 2.0231 1 0.1549
## Origin:Treatment2 1.0392 1 0.3080
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1tukey3<- emmeans(g13824.lme, list(pairwise ~ Origin), adjust = "tukey")## NOTE: Results may be misleading due to involvement in interactionstukey3## $`emmeans of Origin`
## Origin emmean SE df lower.CL upper.CL
## RF 158.76 17.7 19 121.7 195.8
## RS -5.68 17.3 19 -41.9 30.5
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containment
## Confidence level used: 0.95
##
## $`pairwise differences of Origin`
## 1 estimate SE df t.ratio p.value
## RF - RS 164 17 23 9.671 <.0001
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containmentlibrary(Rmisc)
g13824_sum<-summarySE(biomin_all_filtered_long_g13824 , measurevar='Expression', groupvars=c('Origin', 'Treatment2'), na.rm=TRUE, conf.interval = 0.95)
g13824_sum## Origin Treatment2 N Expression sd se ci
## 1 RF Stable 11 156.36191 109.769844 33.096853 73.744384
## 2 RF Variable 11 135.61447 87.446714 26.366176 58.747502
## 3 RS Stable 12 10.39836 9.661042 2.788902 6.138333
## 4 RS Variable 12 10.23764 8.081504 2.332929 5.134743###Figure
pd<- position_dodge(0.2)
g13824_fig<-ggplot(data=g13824_sum, aes(y=Expression, x=Treatment2, color=Origin),group = interaction(Origin))+
geom_point(data=biomin_all_filtered_long_g13824,aes(y=Expression, x=Treatment2, color=Origin), alpha=0.4, position = pd)+
geom_line(aes(group = interaction(Origin), stat="identity"),position=position_dodge(0.2))+
geom_point(size=3, stat="identity", position = pd)+
geom_errorbar(aes(ymin=Expression-se, ymax=Expression+se), stat="identity",width=0.2, position = pd)+
scale_fill_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_color_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_y_continuous(expression(Carbonic~anhydrase~("STPCA2-2")), limits=c(0,300))+
ggtitle(~blue)+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5,size=12),#angling the labels on the x-axis
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),#telling it where to position our plot title
panel.background= element_rect(fill=NA, color='black'),#this is making the black box around the graph
#strip.background = element_blank(),
#strip.text = element_blank(),
legend.title = element_text(vjust=0.5,size=12),
legend.position="none",
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_text(size=12))#making the axis title larger ## Warning in geom_line(aes(group = interaction(Origin), stat = "identity"), :
## Ignoring unknown aesthetics: statg13824_fig## Warning: Removed 1 rows containing missing values (`geom_point()`).
##Mammalian ependymin-related protein 1-like
biomin_all_filtered_long_g25351 <- biomin_all_filtered_long %>%
filter(Gene == "Pocillopora_acuta_HIv2___RNAseq.g25351.t1")
biomin_all_filtered_long_g25351 ## # A tibble: 46 × 36
## Gene Dispersion AIC logLik meanExp X.Intercept. TreatmentVariable
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Pocillopora_a… 0.134 816. -402. 12.2 8.29 -0.0171
## 2 Pocillopora_a… 0.134 816. -402. 12.2 8.29 -0.0171
## 3 Pocillopora_a… 0.134 816. -402. 12.2 8.29 -0.0171
## 4 Pocillopora_a… 0.134 816. -402. 12.2 8.29 -0.0171
## 5 Pocillopora_a… 0.134 816. -402. 12.2 8.29 -0.0171
## 6 Pocillopora_a… 0.134 816. -402. 12.2 8.29 -0.0171
## 7 Pocillopora_a… 0.134 816. -402. 12.2 8.29 -0.0171
## 8 Pocillopora_a… 0.134 816. -402. 12.2 8.29 -0.0171
## 9 Pocillopora_a… 0.134 816. -402. 12.2 8.29 -0.0171
## 10 Pocillopora_a… 0.134 816. -402. 12.2 8.29 -0.0171
## # ℹ 36 more rows
## # ℹ 29 more variables: OriginFlat <dbl>, TreatmentVariable.OriginFlat <dbl>,
## # se_.Intercept. <dbl>, se_TreatmentVariable <dbl>, se_OriginFlat <dbl>,
## # se_TreatmentVariable.OriginFlat <dbl>, Chisq_Treatment <dbl>,
## # Chisq_Origin <dbl>, Chisq_Treatment.Origin <dbl>, Df_Treatment <int>,
## # Df_Origin <int>, Df_Treatment.Origin <int>, P_Treatment <dbl>,
## # P_Origin <dbl>, P_Treatment.Origin <dbl>, Treatment <fct>, …library(nlme)
g25351.lme <- lme(Expression~Origin*Treatment2, random = ~1|Colony, data=biomin_all_filtered_long_g25351 , na.action=na.exclude)
car::Anova(g25351.lme, type=3)## Analysis of Deviance Table (Type III tests)
##
## Response: Expression
## Chisq Df Pr(>Chisq)
## (Intercept) 151.907 1 < 2.2e-16 ***
## Origin 10.058 1 0.001517 **
## Treatment2 1.959 1 0.161619
## Origin:Treatment2 1.039 1 0.308064
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1tukey3<- emmeans(g25351.lme, list(pairwise ~ Origin), adjust = "tukey")## NOTE: Results may be misleading due to involvement in interactionstukey3## $`emmeans of Origin`
## Origin emmean SE df lower.CL upper.CL
## RF 6454 354 19 5713 7195
## RS 3869 339 19 3159 4578
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containment
## Confidence level used: 0.95
##
## $`pairwise differences of Origin`
## 1 estimate SE df t.ratio p.value
## RF - RS 2585 482 23 5.359 <.0001
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containmentlibrary(Rmisc)
g25351_sum<-summarySE(biomin_all_filtered_long_g25351 , measurevar='Expression', groupvars=c('Origin', 'Treatment2'), na.rm=TRUE, conf.interval = 0.95)
g25351_sum## Origin Treatment2 N Expression sd se ci
## 1 RF Stable 11 5958.631 1717.4980 517.8451 1153.8309
## 2 RF Variable 11 6890.207 2342.7581 706.3681 1573.8863
## 3 RS Stable 12 3894.293 756.1492 218.2815 480.4342
## 4 RS Variable 12 3886.639 1300.8557 375.5247 826.5242###Figure
pd<- position_dodge(0.2)
g25351_fig<-ggplot(data=g25351_sum, aes(y=Expression, x=Treatment2, color=Origin),group = interaction(Origin))+
geom_point(data=biomin_all_filtered_long_g25351,aes(y=Expression, x=Treatment2, color=Origin), alpha=0.4, position = pd)+
geom_line(aes(group = interaction(Origin), stat="identity"),position=position_dodge(0.2))+
geom_point(size=3, stat="identity", position = pd)+
geom_errorbar(aes(ymin=Expression-se, ymax=Expression+se), stat="identity",width=0.2, position = pd)+
scale_fill_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_color_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_y_continuous(expression(Mammalian~ependymin-related~protein~1-like),limits=c(2000,10000))+
ggtitle(~blue)+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5,size=12),#angling the labels on the x-axis
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),#telling it where to position our plot title
panel.background= element_rect(fill=NA, color='black'),#this is making the black box around the graph
#strip.background = element_blank(),
#strip.text = element_blank(),
legend.title = element_text(vjust=0.5,size=12),
legend.position="none",
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_text(size=12))#making the axis title larger ## Warning in geom_line(aes(group = interaction(Origin), stat = "identity"), :
## Ignoring unknown aesthetics: statg25351_fig## Warning: Removed 1 rows containing missing values (`geom_point()`).
##Cephalotoxin-like protein
biomin_all_filtered_long_g5013 <- biomin_all_filtered_long %>%
filter(Gene == "Pocillopora_acuta_HIv2___RNAseq.g5013.t1")
biomin_all_filtered_long_g5013 ## # A tibble: 46 × 36
## Gene Dispersion AIC logLik meanExp X.Intercept. TreatmentVariable
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Pocillopora_a… 0.471 304. -146. 3.16 1.83 0.206
## 2 Pocillopora_a… 0.471 304. -146. 3.16 1.83 0.206
## 3 Pocillopora_a… 0.471 304. -146. 3.16 1.83 0.206
## 4 Pocillopora_a… 0.471 304. -146. 3.16 1.83 0.206
## 5 Pocillopora_a… 0.471 304. -146. 3.16 1.83 0.206
## 6 Pocillopora_a… 0.471 304. -146. 3.16 1.83 0.206
## 7 Pocillopora_a… 0.471 304. -146. 3.16 1.83 0.206
## 8 Pocillopora_a… 0.471 304. -146. 3.16 1.83 0.206
## 9 Pocillopora_a… 0.471 304. -146. 3.16 1.83 0.206
## 10 Pocillopora_a… 0.471 304. -146. 3.16 1.83 0.206
## # ℹ 36 more rows
## # ℹ 29 more variables: OriginFlat <dbl>, TreatmentVariable.OriginFlat <dbl>,
## # se_.Intercept. <dbl>, se_TreatmentVariable <dbl>, se_OriginFlat <dbl>,
## # se_TreatmentVariable.OriginFlat <dbl>, Chisq_Treatment <dbl>,
## # Chisq_Origin <dbl>, Chisq_Treatment.Origin <dbl>, Df_Treatment <int>,
## # Df_Origin <int>, Df_Treatment.Origin <int>, P_Treatment <dbl>,
## # P_Origin <dbl>, P_Treatment.Origin <dbl>, Treatment <fct>, …library(nlme)
g5013.lme <- lme(Expression~Origin*Treatment2, random = ~1|Colony, data=biomin_all_filtered_long_g5013 , na.action=na.exclude)
car::Anova(g5013.lme, type=3)## Analysis of Deviance Table (Type III tests)
##
## Response: Expression
## Chisq Df Pr(>Chisq)
## (Intercept) 45.2530 1 1.732e-11 ***
## Origin 6.6236 1 0.01006 *
## Treatment2 0.0840 1 0.77190
## Origin:Treatment2 0.0561 1 0.81279
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1tukey3<- emmeans(g5013.lme, list(pairwise ~ Origin), adjust = "tukey")## NOTE: Results may be misleading due to involvement in interactionstukey3## $`emmeans of Origin`
## Origin emmean SE df lower.CL upper.CL
## RF 13.55 1.49 19 10.43 16.7
## RS 7.14 1.43 19 4.16 10.1
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containment
## Confidence level used: 0.95
##
## $`pairwise differences of Origin`
## 1 estimate SE df t.ratio p.value
## RF - RS 6.41 1.98 23 3.237 0.0036
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containmentlibrary(Rmisc)
g5013_sum<-summarySE(biomin_all_filtered_long_g5013 , measurevar='Expression', groupvars=c('Origin', 'Treatment2'), na.rm=TRUE, conf.interval = 0.95)
g5013_sum## Origin Treatment2 N Expression sd se ci
## 1 RF Stable 11 13.339697 7.878658 2.375505 5.292955
## 2 RF Variable 11 14.078906 6.431123 1.939056 4.320487
## 3 RS Stable 12 6.188827 5.219635 1.506779 3.316398
## 4 RS Variable 12 7.764125 6.413793 1.851503 4.075130###Figure
pd<- position_dodge(0.2)
g5013_fig<-ggplot(data=g5013_sum, aes(y=Expression, x=Treatment2, color=Origin),group = interaction(Origin))+
geom_point(data=biomin_all_filtered_long_g5013,aes(y=Expression, x=Treatment2, color=Origin), alpha=0.4, position = pd)+
geom_line(aes(group = interaction(Origin), stat="identity"),position=position_dodge(0.2))+
geom_point(size=3, stat="identity", position = pd)+
geom_errorbar(aes(ymin=Expression-se, ymax=Expression+se), stat="identity",width=0.2, position = pd)+
scale_fill_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_color_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_y_continuous(expression(Cephalotoxin-like~protein), breaks=c(0,5,10,15,20,25))+
ggtitle(~blue)+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5,size=12),#angling the labels on the x-axis
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),#telling it where to position our plot title
panel.background= element_rect(fill=NA, color='black'),#this is making the black box around the graph
#strip.background = element_blank(),
#strip.text = element_blank(),
legend.title = element_text(vjust=0.5,size=12),
legend.position="none",
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_text(size=12))#making the axis title larger ## Warning in geom_line(aes(group = interaction(Origin), stat = "identity"), :
## Ignoring unknown aesthetics: statg5013_fig
#MEPink signficant genes ##Carbonic anhydrase - STPCA2-1
biomin_all_filtered_long_g12304 <- biomin_all_filtered_long %>%
filter(Gene == "Pocillopora_acuta_HIv2___TS.g12304.t1")
biomin_all_filtered_long_g12304 ## # A tibble: 184 × 36
## Gene Dispersion AIC logLik meanExp X.Intercept. TreatmentVariable
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Pocillopora_a… 0.457 841. -415. 11.6 7.88 0.0448
## 2 Pocillopora_a… 0.457 841. -415. 11.6 7.88 0.0448
## 3 Pocillopora_a… 0.457 841. -415. 11.6 7.88 0.0448
## 4 Pocillopora_a… 0.457 841. -415. 11.6 7.88 0.0448
## 5 Pocillopora_a… 0.457 841. -415. 11.6 7.88 0.0448
## 6 Pocillopora_a… 0.457 841. -415. 11.6 7.88 0.0448
## 7 Pocillopora_a… 0.457 841. -415. 11.6 7.88 0.0448
## 8 Pocillopora_a… 0.457 841. -415. 11.6 7.88 0.0448
## 9 Pocillopora_a… 0.457 841. -415. 11.6 7.88 0.0448
## 10 Pocillopora_a… 0.457 841. -415. 11.6 7.88 0.0448
## # ℹ 174 more rows
## # ℹ 29 more variables: OriginFlat <dbl>, TreatmentVariable.OriginFlat <dbl>,
## # se_.Intercept. <dbl>, se_TreatmentVariable <dbl>, se_OriginFlat <dbl>,
## # se_TreatmentVariable.OriginFlat <dbl>, Chisq_Treatment <dbl>,
## # Chisq_Origin <dbl>, Chisq_Treatment.Origin <dbl>, Df_Treatment <int>,
## # Df_Origin <int>, Df_Treatment.Origin <int>, P_Treatment <dbl>,
## # P_Origin <dbl>, P_Treatment.Origin <dbl>, Treatment <fct>, …library(nlme)
g12304.lme <- lme(Expression~Origin*Treatment2, random = ~1|Colony, data=biomin_all_filtered_long_g12304 , na.action=na.exclude)
car::Anova(g12304.lme, type=3)## Analysis of Deviance Table (Type III tests)
##
## Response: Expression
## Chisq Df Pr(>Chisq)
## (Intercept) 196.964 1 < 2.2e-16 ***
## Origin 55.461 1 9.531e-14 ***
## Treatment2 14.008 1 0.0001820 ***
## Origin:Treatment2 11.399 1 0.0007348 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1tukey3<- emmeans(g12304.lme, list(pairwise ~ Origin), adjust = "tukey")## NOTE: Results may be misleading due to involvement in interactionstukey3## $`emmeans of Origin`
## Origin emmean SE df lower.CL upper.CL
## RF 5238 384 19 4434 6042
## RS 2770 375 19 1985 3555
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containment
## Confidence level used: 0.95
##
## $`pairwise differences of Origin`
## 1 estimate SE df t.ratio p.value
## RF - RS 2468 371 161 6.657 <.0001
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containmentlibrary(Rmisc)
g12304_sum<-summarySE(biomin_all_filtered_long_g12304 , measurevar='Expression', groupvars=c('Origin', 'Treatment2'), na.rm=TRUE, conf.interval = 0.95)
g12304_sum## Origin Treatment2 N Expression sd se ci
## 1 RF Stable 44 5960.191 2423.309 365.3276 736.7533
## 2 RF Variable 44 4766.484 2433.696 366.8934 739.9111
## 3 RS Stable 48 2494.782 1512.223 218.2706 439.1038
## 4 RS Variable 48 2791.885 1392.250 200.9540 404.2674###Figure
pd<- position_dodge(0.2)
g12304_fig<-ggplot(data=g12304_sum, aes(y=Expression, x=Treatment2, color=Origin),group = interaction(Origin))+
geom_point(data=biomin_all_filtered_long_g12304,aes(y=Expression, x=Treatment2, color=Origin), alpha=0.4, position = pd)+
geom_line(aes(group = interaction(Origin), stat="identity"),position=position_dodge(0.2))+
geom_point(size=3, stat="identity", position = pd)+
geom_errorbar(aes(ymin=Expression-se, ymax=Expression+se), stat="identity",width=0.2, position = pd)+
scale_fill_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_color_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_y_continuous(expression(Carbonic~anhydrase~("STPCA2-1")), limits=c(0,10000))+
ggtitle(~blue)+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5,size=12),#angling the labels on the x-axis
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),#telling it where to position our plot title
panel.background= element_rect(fill=NA, color='black'),#this is making the black box around the graph
#strip.background = element_blank(),
#strip.text = element_blank(),
legend.title = element_text(vjust=0.5,size=12),
legend.position="none",
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_text(size=12))#making the axis title larger ## Warning in geom_line(aes(group = interaction(Origin), stat = "identity"), :
## Ignoring unknown aesthetics: statg12304_fig## Warning: Removed 4 rows containing missing values (`geom_point()`).
##SLC4 gamma- solute carrier family 4 member gamma
biomin_all_filtered_long_g15280 <- biomin_all_filtered_long %>%
filter(Gene == "Pocillopora_acuta_HIv2___RNAseq.g15280.t1")
biomin_all_filtered_long_g15280 ## # A tibble: 46 × 36
## Gene Dispersion AIC logLik meanExp X.Intercept. TreatmentVariable
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Pocillopora_a… 0.376 425. -206. 5.12 3.45 0.0890
## 2 Pocillopora_a… 0.376 425. -206. 5.12 3.45 0.0890
## 3 Pocillopora_a… 0.376 425. -206. 5.12 3.45 0.0890
## 4 Pocillopora_a… 0.376 425. -206. 5.12 3.45 0.0890
## 5 Pocillopora_a… 0.376 425. -206. 5.12 3.45 0.0890
## 6 Pocillopora_a… 0.376 425. -206. 5.12 3.45 0.0890
## 7 Pocillopora_a… 0.376 425. -206. 5.12 3.45 0.0890
## 8 Pocillopora_a… 0.376 425. -206. 5.12 3.45 0.0890
## 9 Pocillopora_a… 0.376 425. -206. 5.12 3.45 0.0890
## 10 Pocillopora_a… 0.376 425. -206. 5.12 3.45 0.0890
## # ℹ 36 more rows
## # ℹ 29 more variables: OriginFlat <dbl>, TreatmentVariable.OriginFlat <dbl>,
## # se_.Intercept. <dbl>, se_TreatmentVariable <dbl>, se_OriginFlat <dbl>,
## # se_TreatmentVariable.OriginFlat <dbl>, Chisq_Treatment <dbl>,
## # Chisq_Origin <dbl>, Chisq_Treatment.Origin <dbl>, Df_Treatment <int>,
## # Df_Origin <int>, Df_Treatment.Origin <int>, P_Treatment <dbl>,
## # P_Origin <dbl>, P_Treatment.Origin <dbl>, Treatment <fct>, …library(nlme)
g15280.lme <- lme(Expression~Origin*Treatment2, random = ~1|Colony, data=biomin_all_filtered_long_g15280 , na.action=na.exclude)
car::Anova(g15280.lme, type=3)## Analysis of Deviance Table (Type III tests)
##
## Response: Expression
## Chisq Df Pr(>Chisq)
## (Intercept) 82.1177 1 < 2.2e-16 ***
## Origin 9.0855 1 0.002576 **
## Treatment2 0.7652 1 0.381698
## Origin:Treatment2 0.9266 1 0.335743
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1tukey3<- emmeans(g15280.lme, list(pairwise ~ Origin), adjust = "tukey")## NOTE: Results may be misleading due to involvement in interactionstukey3## $`emmeans of Origin`
## Origin emmean SE df lower.CL upper.CL
## RF 52.0 4.36 19 42.9 61.2
## RS 32.1 4.17 19 23.4 40.9
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containment
## Confidence level used: 0.95
##
## $`pairwise differences of Origin`
## 1 estimate SE df t.ratio p.value
## RF - RS 19.9 6.03 23 3.300 0.0031
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containmentlibrary(Rmisc)
g15280_sum<-summarySE(biomin_all_filtered_long_g15280 , measurevar='Expression', groupvars=c('Origin', 'Treatment2'), na.rm=TRUE, conf.interval = 0.95)
g15280_sum## Origin Treatment2 N Expression sd se ci
## 1 RF Stable 11 55.84385 24.85863 7.495159 16.700254
## 2 RF Variable 11 48.22013 24.68527 7.442889 16.583790
## 3 RS Stable 12 30.12777 14.24152 4.111172 9.048629
## 4 RS Variable 12 34.11841 16.62673 4.799723 10.564118###Figure
pd<- position_dodge(0.2)
g15280_fig<-ggplot(data=g15280_sum, aes(y=Expression, x=Treatment2, color=Origin),group = interaction(Origin))+
geom_point(data=biomin_all_filtered_long_g15280,aes(y=Expression, x=Treatment2, color=Origin), alpha=0.4, position = pd)+
geom_line(aes(group = interaction(Origin), stat="identity"),position=position_dodge(0.2))+
geom_point(size=3, stat="identity", position = pd)+
geom_errorbar(aes(ymin=Expression-se, ymax=Expression+se), stat="identity",width=0.2, position = pd)+
scale_fill_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_color_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_y_continuous(expression(Solute~carrier~family~4~member~gamma))+
ggtitle(~blue)+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5,size=12),#angling the labels on the x-axis
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),#telling it where to position our plot title
panel.background= element_rect(fill=NA, color='black'),#this is making the black box around the graph
#strip.background = element_blank(),
#strip.text = element_blank(),
legend.title = element_text(vjust=0.5,size=12),
legend.position="none",
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_text(size=12))#making the axis title larger ## Warning in geom_line(aes(group = interaction(Origin), stat = "identity"), :
## Ignoring unknown aesthetics: statg15280_fig
##SLC4A7 - sodium bicarbonate cotransporter 3-like isoform X2
biomin_all_filtered_long_g7402 <- biomin_all_filtered_long %>%
filter(Gene == "Pocillopora_acuta_HIv2___RNAseq.g7402.t1")
biomin_all_filtered_long_g7402 ## # A tibble: 46 × 36
## Gene Dispersion AIC logLik meanExp X.Intercept. TreatmentVariable
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Pocillopora_a… 0.229 640. -314. 8.97 6.14 0.0129
## 2 Pocillopora_a… 0.229 640. -314. 8.97 6.14 0.0129
## 3 Pocillopora_a… 0.229 640. -314. 8.97 6.14 0.0129
## 4 Pocillopora_a… 0.229 640. -314. 8.97 6.14 0.0129
## 5 Pocillopora_a… 0.229 640. -314. 8.97 6.14 0.0129
## 6 Pocillopora_a… 0.229 640. -314. 8.97 6.14 0.0129
## 7 Pocillopora_a… 0.229 640. -314. 8.97 6.14 0.0129
## 8 Pocillopora_a… 0.229 640. -314. 8.97 6.14 0.0129
## 9 Pocillopora_a… 0.229 640. -314. 8.97 6.14 0.0129
## 10 Pocillopora_a… 0.229 640. -314. 8.97 6.14 0.0129
## # ℹ 36 more rows
## # ℹ 29 more variables: OriginFlat <dbl>, TreatmentVariable.OriginFlat <dbl>,
## # se_.Intercept. <dbl>, se_TreatmentVariable <dbl>, se_OriginFlat <dbl>,
## # se_TreatmentVariable.OriginFlat <dbl>, Chisq_Treatment <dbl>,
## # Chisq_Origin <dbl>, Chisq_Treatment.Origin <dbl>, Df_Treatment <int>,
## # Df_Origin <int>, Df_Treatment.Origin <int>, P_Treatment <dbl>,
## # P_Origin <dbl>, P_Treatment.Origin <dbl>, Treatment <fct>, …library(nlme)
g7402.lme <- lme(Expression~Origin*Treatment2, random = ~1|Colony, data=biomin_all_filtered_long_g7402 , na.action=na.exclude)
car::Anova(g7402.lme, type=3)## Analysis of Deviance Table (Type III tests)
##
## Response: Expression
## Chisq Df Pr(>Chisq)
## (Intercept) 87.9465 1 <2e-16 ***
## Origin 6.3555 1 0.0117 *
## Treatment2 0.8936 1 0.3445
## Origin:Treatment2 0.8273 1 0.3630
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1tukey3<- emmeans(g7402.lme, list(pairwise ~ Origin), adjust = "tukey")## NOTE: Results may be misleading due to involvement in interactionstukey3## $`emmeans of Origin`
## Origin emmean SE df lower.CL upper.CL
## RF 660 54.9 19 545 775
## RS 464 52.6 19 353 574
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containment
## Confidence level used: 0.95
##
## $`pairwise differences of Origin`
## 1 estimate SE df t.ratio p.value
## RF - RS 197 75 23 2.621 0.0153
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containmentlibrary(Rmisc)
g7402_sum<-summarySE(biomin_all_filtered_long_g7402 , measurevar='Expression', groupvars=c('Origin', 'Treatment2'), na.rm=TRUE, conf.interval = 0.95)
g7402_sum## Origin Treatment2 N Expression sd se ci
## 1 RF Stable 11 710.2028 264.1958 79.65802 177.4891
## 2 RF Variable 11 611.9007 312.5396 94.23425 209.9670
## 3 RS Stable 12 445.6090 228.0413 65.82984 144.8905
## 4 RS Variable 12 478.2523 190.4959 54.99144 121.0353###Figure
pd<- position_dodge(0.2)
g7402_fig<-ggplot(data=g7402_sum, aes(y=Expression, x=Treatment2, color=Origin),group = interaction(Origin))+
geom_point(data=biomin_all_filtered_long_g7402,aes(y=Expression, x=Treatment2, color=Origin), alpha=0.4, position = pd)+
geom_line(aes(group = interaction(Origin), stat="identity"),position=position_dodge(0.2))+
geom_point(size=3, stat="identity", position = pd)+
geom_errorbar(aes(ymin=Expression-se, ymax=Expression+se), stat="identity",width=0.2, position = pd)+
scale_fill_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_color_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_y_continuous(expression(sodium~bicarbonate~cotransporter~3-like~isoform~X2))+
ggtitle(~blue)+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5,size=12),#angling the labels on the x-axis
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),#telling it where to position our plot title
panel.background= element_rect(fill=NA, color='black'),#this is making the black box around the graph
#strip.background = element_blank(),
#strip.text = element_blank(),
legend.title = element_text(vjust=0.5,size=12),
legend.position="none",
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_text(size=12))#making the axis title larger ## Warning in geom_line(aes(group = interaction(Origin), stat = "identity"), :
## Ignoring unknown aesthetics: statg7402_fig
##Protein lingerer-like
biomin_all_filtered_long_g7908 <- biomin_all_filtered_long %>%
filter(Gene == "Pocillopora_acuta_HIv2___RNAseq.g7908.t1")
biomin_all_filtered_long_g7908 ## # A tibble: 46 × 36
## Gene Dispersion AIC logLik meanExp X.Intercept. TreatmentVariable
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Pocillopora_a… 0.138 426. -207. 5.95 3.98 -0.0743
## 2 Pocillopora_a… 0.138 426. -207. 5.95 3.98 -0.0743
## 3 Pocillopora_a… 0.138 426. -207. 5.95 3.98 -0.0743
## 4 Pocillopora_a… 0.138 426. -207. 5.95 3.98 -0.0743
## 5 Pocillopora_a… 0.138 426. -207. 5.95 3.98 -0.0743
## 6 Pocillopora_a… 0.138 426. -207. 5.95 3.98 -0.0743
## 7 Pocillopora_a… 0.138 426. -207. 5.95 3.98 -0.0743
## 8 Pocillopora_a… 0.138 426. -207. 5.95 3.98 -0.0743
## 9 Pocillopora_a… 0.138 426. -207. 5.95 3.98 -0.0743
## 10 Pocillopora_a… 0.138 426. -207. 5.95 3.98 -0.0743
## # ℹ 36 more rows
## # ℹ 29 more variables: OriginFlat <dbl>, TreatmentVariable.OriginFlat <dbl>,
## # se_.Intercept. <dbl>, se_TreatmentVariable <dbl>, se_OriginFlat <dbl>,
## # se_TreatmentVariable.OriginFlat <dbl>, Chisq_Treatment <dbl>,
## # Chisq_Origin <dbl>, Chisq_Treatment.Origin <dbl>, Df_Treatment <int>,
## # Df_Origin <int>, Df_Treatment.Origin <int>, P_Treatment <dbl>,
## # P_Origin <dbl>, P_Treatment.Origin <dbl>, Treatment <fct>, …library(nlme)
g7908.lme <- lme(Expression~Origin*Treatment2, random = ~1|Colony, data=biomin_all_filtered_long_g7908 , na.action=na.exclude)
car::Anova(g7908.lme, type=3)## Analysis of Deviance Table (Type III tests)
##
## Response: Expression
## Chisq Df Pr(>Chisq)
## (Intercept) 207.4212 1 < 2.2e-16 ***
## Origin 15.8613 1 6.816e-05 ***
## Treatment2 0.1605 1 0.6887
## Origin:Treatment2 0.0058 1 0.9392
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1tukey3<- emmeans(g7908.lme, list(pairwise ~ Origin), adjust = "tukey")## NOTE: Results may be misleading due to involvement in interactionstukey3## $`emmeans of Origin`
## Origin emmean SE df lower.CL upper.CL
## RF 81.2 4.07 19 72.7 89.7
## RS 49.9 3.89 19 41.8 58.0
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containment
## Confidence level used: 0.95
##
## $`pairwise differences of Origin`
## 1 estimate SE df t.ratio p.value
## RF - RS 31.3 5.63 23 5.556 <.0001
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containmentlibrary(Rmisc)
g7908_sum<-summarySE(biomin_all_filtered_long_g7908 , measurevar='Expression', groupvars=c('Origin', 'Treatment2'), na.rm=TRUE, conf.interval = 0.95)
g7908_sum## Origin Treatment2 N Expression sd se ci
## 1 RF Stable 11 82.80022 22.33628 6.734642 15.005717
## 2 RF Variable 11 79.54283 21.44921 6.467180 14.409774
## 3 RS Stable 12 51.10111 16.98594 4.903419 10.792352
## 4 RS Variable 12 48.70220 15.09645 4.357969 9.591824###Figure
pd<- position_dodge(0.2)
g7908_fig<-ggplot(data=g7908_sum, aes(y=Expression, x=Treatment2, color=Origin),group = interaction(Origin))+
geom_point(data=biomin_all_filtered_long_g7908,aes(y=Expression, x=Treatment2, color=Origin), alpha=0.4, position = pd)+
geom_line(aes(group = interaction(Origin), stat="identity"),position=position_dodge(0.2))+
geom_point(size=3, stat="identity", position = pd)+
geom_errorbar(aes(ymin=Expression-se, ymax=Expression+se), stat="identity",width=0.2, position = pd)+
scale_fill_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_color_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_y_continuous(expression(protein~lingerer-like))+
ggtitle(~blue)+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5,size=12),#angling the labels on the x-axis
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),#telling it where to position our plot title
panel.background= element_rect(fill=NA, color='black'),#this is making the black box around the graph
#strip.background = element_blank(),
#strip.text = element_blank(),
legend.title = element_text(vjust=0.5,size=12),
legend.position="none",
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_text(size=12))#making the axis title larger ## Warning in geom_line(aes(group = interaction(Origin), stat = "identity"), :
## Ignoring unknown aesthetics: statg7908_fig
#Signficant genes not in WGCNA modules ##Vitellogenin
biomin_all_filtered_long_g13222 <- biomin_all_filtered_long %>%
filter(Gene == "Pocillopora_acuta_HIv2___TS.g13222.t1b")
biomin_all_filtered_long_g13222 ## # A tibble: 184 × 36
## Gene Dispersion AIC logLik meanExp X.Intercept. TreatmentVariable
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Pocillopora_a… 0.0506 621. -305. 9.50 6.53 -0.123
## 2 Pocillopora_a… 0.0506 621. -305. 9.50 6.53 -0.123
## 3 Pocillopora_a… 0.0506 621. -305. 9.50 6.53 -0.123
## 4 Pocillopora_a… 0.0506 621. -305. 9.50 6.53 -0.123
## 5 Pocillopora_a… 0.0506 621. -305. 9.50 6.53 -0.123
## 6 Pocillopora_a… 0.0506 621. -305. 9.50 6.53 -0.123
## 7 Pocillopora_a… 0.0506 621. -305. 9.50 6.53 -0.123
## 8 Pocillopora_a… 0.0506 621. -305. 9.50 6.53 -0.123
## 9 Pocillopora_a… 0.0506 621. -305. 9.50 6.53 -0.123
## 10 Pocillopora_a… 0.0506 621. -305. 9.50 6.53 -0.123
## # ℹ 174 more rows
## # ℹ 29 more variables: OriginFlat <dbl>, TreatmentVariable.OriginFlat <dbl>,
## # se_.Intercept. <dbl>, se_TreatmentVariable <dbl>, se_OriginFlat <dbl>,
## # se_TreatmentVariable.OriginFlat <dbl>, Chisq_Treatment <dbl>,
## # Chisq_Origin <dbl>, Chisq_Treatment.Origin <dbl>, Df_Treatment <int>,
## # Df_Origin <int>, Df_Treatment.Origin <int>, P_Treatment <dbl>,
## # P_Origin <dbl>, P_Treatment.Origin <dbl>, Treatment <fct>, …library(nlme)
g13222.lme <- lme(Expression~Origin*Treatment2, random = ~1|Colony, data=biomin_all_filtered_long_g13222 , na.action=na.exclude)
car::Anova(g13222.lme, type=3)## Analysis of Deviance Table (Type III tests)
##
## Response: Expression
## Chisq Df Pr(>Chisq)
## (Intercept) 1126.7286 1 < 2.2e-16 ***
## Origin 41.2035 1 1.372e-10 ***
## Treatment2 2.9349 1 0.08669 .
## Origin:Treatment2 0.5477 1 0.45926
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1tukey3<- emmeans(g13222.lme, list(pairwise ~ Origin), adjust = "tukey")## NOTE: Results may be misleading due to involvement in interactionstukey3## $`emmeans of Origin`
## Origin emmean SE df lower.CL upper.CL
## RF 832 22.8 19 784 879
## RS 636 22.2 19 590 683
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containment
## Confidence level used: 0.95
##
## $`pairwise differences of Origin`
## 1 estimate SE df t.ratio p.value
## RF - RS 195 24.2 161 8.053 <.0001
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containmentlibrary(Rmisc)
g13222_sum<-summarySE(biomin_all_filtered_long_g13222 , measurevar='Expression', groupvars=c('Origin', 'Treatment2'), na.rm=TRUE, conf.interval = 0.95)
g13222_sum## Origin Treatment2 N Expression sd se ci
## 1 RF Stable 44 859.5886 158.58611 23.90776 48.21459
## 2 RF Variable 44 821.8027 114.92648 17.32582 34.94084
## 3 RS Stable 48 660.1489 146.62900 21.16407 42.57662
## 4 RS Variable 48 599.7645 70.60441 10.19087 20.50138###Figure
pd<- position_dodge(0.2)
g13222_fig<-ggplot(data=g13222_sum, aes(y=Expression, x=Treatment2, color=Origin),group = interaction(Origin))+
geom_point(data=biomin_all_filtered_long_g13222,aes(y=Expression, x=Treatment2, color=Origin), alpha=0.4, position = pd)+
geom_line(aes(group = interaction(Origin), stat="identity"),position=position_dodge(0.2))+
geom_point(size=3, stat="identity", position = pd)+
geom_errorbar(aes(ymin=Expression-se, ymax=Expression+se), stat="identity",width=0.2, position = pd)+
scale_fill_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_color_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_y_continuous(expression(Vitellogenin))+
ggtitle(~blue)+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5,size=12),#angling the labels on the x-axis
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),#telling it where to position our plot title
panel.background= element_rect(fill=NA, color='black'),#this is making the black box around the graph
#strip.background = element_blank(),
#strip.text = element_blank(),
legend.title = element_text(vjust=0.5,size=12),
legend.position="none",
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_text(size=12))#making the axis title larger ## Warning in geom_line(aes(group = interaction(Origin), stat = "identity"), :
## Ignoring unknown aesthetics: statg13222_fig
##uncharacterized protein LOC111323869
biomin_all_filtered_long_g21232 <- biomin_all_filtered_long %>%
filter(Gene == "Pocillopora_acuta_HIv2___RNAseq.g21232.t1")
biomin_all_filtered_long_g21232 ## # A tibble: 46 × 36
## Gene Dispersion AIC logLik meanExp X.Intercept. TreatmentVariable
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Pocillopora_a… 0.0605 353. -171. 5.22 3.54 -0.0600
## 2 Pocillopora_a… 0.0605 353. -171. 5.22 3.54 -0.0600
## 3 Pocillopora_a… 0.0605 353. -171. 5.22 3.54 -0.0600
## 4 Pocillopora_a… 0.0605 353. -171. 5.22 3.54 -0.0600
## 5 Pocillopora_a… 0.0605 353. -171. 5.22 3.54 -0.0600
## 6 Pocillopora_a… 0.0605 353. -171. 5.22 3.54 -0.0600
## 7 Pocillopora_a… 0.0605 353. -171. 5.22 3.54 -0.0600
## 8 Pocillopora_a… 0.0605 353. -171. 5.22 3.54 -0.0600
## 9 Pocillopora_a… 0.0605 353. -171. 5.22 3.54 -0.0600
## 10 Pocillopora_a… 0.0605 353. -171. 5.22 3.54 -0.0600
## # ℹ 36 more rows
## # ℹ 29 more variables: OriginFlat <dbl>, TreatmentVariable.OriginFlat <dbl>,
## # se_.Intercept. <dbl>, se_TreatmentVariable <dbl>, se_OriginFlat <dbl>,
## # se_TreatmentVariable.OriginFlat <dbl>, Chisq_Treatment <dbl>,
## # Chisq_Origin <dbl>, Chisq_Treatment.Origin <dbl>, Df_Treatment <int>,
## # Df_Origin <int>, Df_Treatment.Origin <int>, P_Treatment <dbl>,
## # P_Origin <dbl>, P_Treatment.Origin <dbl>, Treatment <fct>, …library(nlme)
g21232.lme <- lme(Expression~Origin*Treatment2, random = ~1|Colony, data=biomin_all_filtered_long_g21232 , na.action=na.exclude)
car::Anova(g21232.lme, type=3)## Analysis of Deviance Table (Type III tests)
##
## Response: Expression
## Chisq Df Pr(>Chisq)
## (Intercept) 209.9697 1 < 2e-16 ***
## Origin 4.7421 1 0.02943 *
## Treatment2 0.1307 1 0.71769
## Origin:Treatment2 0.0003 1 0.98700
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1tukey3<- emmeans(g21232.lme, list(pairwise ~ Origin), adjust = "tukey")## NOTE: Results may be misleading due to involvement in interactionstukey3## $`emmeans of Origin`
## Origin emmean SE df lower.CL upper.CL
## RF 42.0 2.4 19 36.9 47.0
## RS 33.7 2.3 19 28.8 38.5
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containment
## Confidence level used: 0.95
##
## $`pairwise differences of Origin`
## 1 estimate SE df t.ratio p.value
## RF - RS 8.29 3.02 23 2.747 0.0115
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containmentlibrary(Rmisc)
g21232_sum<-summarySE(biomin_all_filtered_long_g21232 , measurevar='Expression', groupvars=c('Origin', 'Treatment2'), na.rm=TRUE, conf.interval = 0.95)
g21232_sum## Origin Treatment2 N Expression sd se ci
## 1 RF Stable 11 42.29276 10.185331 3.070993 6.842599
## 2 RF Variable 11 41.06536 11.600467 3.497672 7.793300
## 3 RS Stable 12 33.84473 7.075632 2.042559 4.495642
## 4 RS Variable 12 32.69394 10.921097 3.152649 6.938934###Figure
pd<- position_dodge(0.2)
g21232_fig<-ggplot(data=g21232_sum, aes(y=Expression, x=Treatment2, color=Origin),group = interaction(Origin))+
geom_point(data=biomin_all_filtered_long_g21232,aes(y=Expression, x=Treatment2, color=Origin), alpha=0.4, position = pd)+
geom_line(aes(group = interaction(Origin), stat="identity"),position=position_dodge(0.2))+
geom_point(size=3, stat="identity", position = pd)+
geom_errorbar(aes(ymin=Expression-se, ymax=Expression+se), stat="identity",width=0.2, position = pd)+
scale_fill_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_color_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_y_continuous(expression(uncharacterized~protein~LOC111323869))+
ggtitle(~blue)+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5,size=12),#angling the labels on the x-axis
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),#telling it where to position our plot title
panel.background= element_rect(fill=NA, color='black'),#this is making the black box around the graph
#strip.background = element_blank(),
#strip.text = element_blank(),
legend.title = element_text(vjust=0.5,size=12),
legend.position="none",
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_text(size=12))#making the axis title larger ## Warning in geom_line(aes(group = interaction(Origin), stat = "identity"), :
## Ignoring unknown aesthetics: statg21232_fig
##uncharacterized protein LOC111345150
biomin_all_filtered_long_g20587 <- biomin_all_filtered_long %>%
filter(Gene == "Pocillopora_acuta_HIv2___RNAseq.g20587.t2")
biomin_all_filtered_long_g20587 ## # A tibble: 46 × 36
## Gene Dispersion AIC logLik meanExp X.Intercept. TreatmentVariable
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Pocillopora_a… 4.85 271. -129. 1.93 2.59 0.106
## 2 Pocillopora_a… 4.85 271. -129. 1.93 2.59 0.106
## 3 Pocillopora_a… 4.85 271. -129. 1.93 2.59 0.106
## 4 Pocillopora_a… 4.85 271. -129. 1.93 2.59 0.106
## 5 Pocillopora_a… 4.85 271. -129. 1.93 2.59 0.106
## 6 Pocillopora_a… 4.85 271. -129. 1.93 2.59 0.106
## 7 Pocillopora_a… 4.85 271. -129. 1.93 2.59 0.106
## 8 Pocillopora_a… 4.85 271. -129. 1.93 2.59 0.106
## 9 Pocillopora_a… 4.85 271. -129. 1.93 2.59 0.106
## 10 Pocillopora_a… 4.85 271. -129. 1.93 2.59 0.106
## # ℹ 36 more rows
## # ℹ 29 more variables: OriginFlat <dbl>, TreatmentVariable.OriginFlat <dbl>,
## # se_.Intercept. <dbl>, se_TreatmentVariable <dbl>, se_OriginFlat <dbl>,
## # se_TreatmentVariable.OriginFlat <dbl>, Chisq_Treatment <dbl>,
## # Chisq_Origin <dbl>, Chisq_Treatment.Origin <dbl>, Df_Treatment <int>,
## # Df_Origin <int>, Df_Treatment.Origin <int>, P_Treatment <dbl>,
## # P_Origin <dbl>, P_Treatment.Origin <dbl>, Treatment <fct>, …library(nlme)
g20587.lme <- lme(Expression~Origin*Treatment2, random = ~1|Colony, data=biomin_all_filtered_long_g20587 , na.action=na.exclude)
car::Anova(g20587.lme, type=3)## Analysis of Deviance Table (Type III tests)
##
## Response: Expression
## Chisq Df Pr(>Chisq)
## (Intercept) 0.1659 1 0.683767
## Origin 7.2048 1 0.007271 **
## Treatment2 0.1684 1 0.681502
## Origin:Treatment2 0.0040 1 0.949524
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1tukey3<- emmeans(g20587.lme, list(pairwise ~ Origin), adjust = "tukey")## NOTE: Results may be misleading due to involvement in interactionstukey3## $`emmeans of Origin`
## Origin emmean SE df lower.CL upper.CL
## RF 2.06 2.78 19 -3.77 7.88
## RS 13.31 2.68 19 7.70 18.93
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containment
## Confidence level used: 0.95
##
## $`pairwise differences of Origin`
## 1 estimate SE df t.ratio p.value
## RF - RS -11.3 3.35 23 -3.355 0.0027
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containmentlibrary(Rmisc)
g20587_sum<-summarySE(biomin_all_filtered_long_g20587 , measurevar='Expression', groupvars=c('Origin', 'Treatment2'), na.rm=TRUE, conf.interval = 0.95)
g20587_sum## Origin Treatment2 N Expression sd se ci
## 1 RF Stable 11 1.069422 2.379314 0.7173901 1.598445
## 2 RF Variable 11 2.503911 3.677310 1.1087507 2.470451
## 3 RS Stable 12 12.756815 15.369960 4.4369253 9.765607
## 4 RS Variable 12 14.497631 15.007069 4.3321675 9.535036###Figure
pd<- position_dodge(0.2)
g20587_fig<-ggplot(data=g20587_sum, aes(y=Expression, x=Treatment2, color=Origin),group = interaction(Origin))+
geom_point(data=biomin_all_filtered_long_g20587,aes(y=Expression, x=Treatment2, color=Origin), alpha=0.4, position = pd)+
geom_line(aes(group = interaction(Origin), stat="identity"),position=position_dodge(0.2))+
geom_point(size=3, stat="identity", position = pd)+
geom_errorbar(aes(ymin=Expression-se, ymax=Expression+se), stat="identity",width=0.2, position = pd)+
scale_fill_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_color_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_y_continuous(expression(uncharacterized~protein~LOC111345150), limits=c(0,30))+
ggtitle(~blue)+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5,size=12),#angling the labels on the x-axis
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),#telling it where to position our plot title
panel.background= element_rect(fill=NA, color='black'),#this is making the black box around the graph
#strip.background = element_blank(),
#strip.text = element_blank(),
legend.title = element_text(vjust=0.5,size=12),
legend.position="none",
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_text(size=12))#making the axis title larger ## Warning in geom_line(aes(group = interaction(Origin), stat = "identity"), :
## Ignoring unknown aesthetics: statg20587_fig## Warning: Removed 4 rows containing missing values (`geom_point()`).
##Late embryogenesis protein
biomin_all_filtered_long_g16715 <- biomin_all_filtered_long %>%
filter(Gene == "Pocillopora_acuta_HIv2___RNAseq.g16715.t1")
biomin_all_filtered_long_g16715 ## # A tibble: 46 × 36
## Gene Dispersion AIC logLik meanExp X.Intercept. TreatmentVariable
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Pocillopora_a… 0.154 847. -417. 12.6 8.39 0.255
## 2 Pocillopora_a… 0.154 847. -417. 12.6 8.39 0.255
## 3 Pocillopora_a… 0.154 847. -417. 12.6 8.39 0.255
## 4 Pocillopora_a… 0.154 847. -417. 12.6 8.39 0.255
## 5 Pocillopora_a… 0.154 847. -417. 12.6 8.39 0.255
## 6 Pocillopora_a… 0.154 847. -417. 12.6 8.39 0.255
## 7 Pocillopora_a… 0.154 847. -417. 12.6 8.39 0.255
## 8 Pocillopora_a… 0.154 847. -417. 12.6 8.39 0.255
## 9 Pocillopora_a… 0.154 847. -417. 12.6 8.39 0.255
## 10 Pocillopora_a… 0.154 847. -417. 12.6 8.39 0.255
## # ℹ 36 more rows
## # ℹ 29 more variables: OriginFlat <dbl>, TreatmentVariable.OriginFlat <dbl>,
## # se_.Intercept. <dbl>, se_TreatmentVariable <dbl>, se_OriginFlat <dbl>,
## # se_TreatmentVariable.OriginFlat <dbl>, Chisq_Treatment <dbl>,
## # Chisq_Origin <dbl>, Chisq_Treatment.Origin <dbl>, Df_Treatment <int>,
## # Df_Origin <int>, Df_Treatment.Origin <int>, P_Treatment <dbl>,
## # P_Origin <dbl>, P_Treatment.Origin <dbl>, Treatment <fct>, …library(nlme)
g16715.lme <- lme(Expression~Origin*Treatment2, random = ~1|Colony, data=biomin_all_filtered_long_g16715 , na.action=na.exclude)
car::Anova(g16715.lme, type=3)## Analysis of Deviance Table (Type III tests)
##
## Response: Expression
## Chisq Df Pr(>Chisq)
## (Intercept) 265.1538 1 < 2.2e-16 ***
## Origin 32.7124 1 1.069e-08 ***
## Treatment2 0.3604 1 0.5483
## Origin:Treatment2 1.3445 1 0.2462
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1tukey3<- emmeans(g16715.lme, list(pairwise ~ Origin), adjust = "tukey")## NOTE: Results may be misleading due to involvement in interactionstukey3## $`emmeans of Origin`
## Origin emmean SE df lower.CL upper.CL
## RF 8304 381 19 7507 9101
## RS 4973 365 19 4209 5737
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containment
## Confidence level used: 0.95
##
## $`pairwise differences of Origin`
## 1 estimate SE df t.ratio p.value
## RF - RS 3331 505 23 6.602 <.0001
##
## Results are averaged over the levels of: Treatment2
## Degrees-of-freedom method: containmentlibrary(Rmisc)
g16715_sum<-summarySE(biomin_all_filtered_long_g16715 , measurevar='Expression', groupvars=c('Origin', 'Treatment2'), na.rm=TRUE, conf.interval = 0.95)
g16715_sum## Origin Treatment2 N Expression sd se ci
## 1 RF Stable 11 8076.757 1731.637 522.1082 1163.3295
## 2 RF Variable 11 8462.423 1729.677 521.5172 1162.0128
## 3 RS Stable 12 4230.613 1879.259 542.4954 1194.0243
## 4 RS Variable 12 5647.539 1237.158 357.1369 786.0529###Figure
pd<- position_dodge(0.2)
g16715_fig<-ggplot(data=g16715_sum, aes(y=Expression, x=Treatment2, color=Origin),group = interaction(Origin))+
geom_point(data=biomin_all_filtered_long_g16715,aes(y=Expression, x=Treatment2, color=Origin), alpha=0.4, position = pd)+
geom_line(aes(group = interaction(Origin), stat="identity"),position=position_dodge(0.2))+
geom_point(size=3, stat="identity", position = pd)+
geom_errorbar(aes(ymin=Expression-se, ymax=Expression+se), stat="identity",width=0.2, position = pd)+
scale_fill_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_color_manual("Origin", values=c("RS"='#26519B', "RF"= "#FE180C"))+
scale_y_continuous(expression(Late~embryogenesis~protein))+
ggtitle(~blue)+
theme_classic()+
theme(axis.text.x=element_text(vjust=0.5,size=12),#angling the labels on the x-axis
plot.title = element_text(margin = margin(t = 10, b = 10), hjust=0.5),#telling it where to position our plot title
panel.background= element_rect(fill=NA, color='black'),#this is making the black box around the graph
#strip.background = element_blank(),
#strip.text = element_blank(),
legend.title = element_text(vjust=0.5,size=12),
legend.position="none",
axis.text.y = element_text(vjust=0.5, size=12), #making the axis text larger
axis.title.x = element_blank(),#making the axis title larger
axis.title.y = element_text(size=12))#making the axis title larger ## Warning in geom_line(aes(group = interaction(Origin), stat = "identity"), :
## Ignoring unknown aesthetics: statg16715_fig
#Comparison of all sig. genes
biomin_compare_figs<-cowplot::plot_grid(g13824_fig,g25351_fig,g10093_fig,g5013_fig, g12304_fig,g7908_fig,g12304_fig,g13222_fig,g16715_fig,g20587_fig,g21232_fig,g15280_fig,g7402_fig, nrow=4)## Warning: Removed 1 rows containing missing values (`geom_point()`).
## Removed 1 rows containing missing values (`geom_point()`).## Warning: Removed 4 rows containing missing values (`geom_point()`).
## Removed 4 rows containing missing values (`geom_point()`).
## Removed 4 rows containing missing values (`geom_point()`).biomin_compare_figs